From 88f4297e39d09eb4a0ce9ee960483b0f9e171097 Mon Sep 17 00:00:00 2001 From: Nantia Leonidou Date: Thu, 20 Apr 2023 08:10:11 +0200 Subject: [PATCH] re-arrange directories to ensure package is pip-installable and executable --- pymcadre/__init__.py | 2 + pymcadre/check/__init__.py | 2 + pymcadre/check/check_model_function.py | 115 + pymcadre/check/check_rxn_flux.py | 83 + pymcadre/check/find_ex_reactions.py | 26 + pymcadre/check/find_organic_ex_rxns.py | 45 + pymcadre/check/find_required_rxns.py | 70 + pymcadre/check/set_metabolite_bounds.py | 40 + pymcadre/code_organization.txt | 32 + pymcadre/main_pymcadre.ipynb | 214 + pymcadre/main_pymcadre.py | 66 + pymcadre/prune/__init__.py | 2 + pymcadre/prune/check_core_deadends.py | 93 + pymcadre/prune/check_model_consistency.py | 82 + pymcadre/prune/check_salvage_path.py | 103 + pymcadre/prune/find_inactive_rxns.py | 69 + pymcadre/prune/prune_model.py | 163 + pymcadre/rank/__init__.py | 2 + pymcadre/rank/calc_conn_evidence.py | 50 + pymcadre/rank/calc_expr_evidence.py | 55 + pymcadre/rank/initialize_generic_model.py | 82 + pymcadre/rank/map_gene_scores_to_rxns.py | 58 + pymcadre/rank/map_high_conf_to_rxns.py | 68 + pymcadre/rank/parse_gprs.py | 70 + pymcadre/rank/rank_reactions.py | 121 + ...con1_with_BOF_and_VBOF__BEC1_method2.ipynb | 16222 ++++++++++++++++ .../test_check_model_consistency_module.ipynb | 283 + pymcadre/test_scripts/test_check_module.ipynb | 315 + .../test_prune_model_fastcc.ipynb | 168 + .../test_prune_module_fastFVA.ipynb | 168 + .../test_rank_reactions_module.ipynb | 365 + 31 files changed, 19234 insertions(+) create mode 100644 pymcadre/__init__.py create mode 100644 pymcadre/check/__init__.py create mode 100644 pymcadre/check/check_model_function.py create mode 100644 pymcadre/check/check_rxn_flux.py create mode 100644 pymcadre/check/find_ex_reactions.py create mode 100644 pymcadre/check/find_organic_ex_rxns.py create mode 100644 pymcadre/check/find_required_rxns.py create mode 100644 pymcadre/check/set_metabolite_bounds.py create mode 100644 pymcadre/code_organization.txt create mode 100644 pymcadre/main_pymcadre.ipynb create mode 100644 pymcadre/main_pymcadre.py create mode 100644 pymcadre/prune/__init__.py create mode 100644 pymcadre/prune/check_core_deadends.py create mode 100644 pymcadre/prune/check_model_consistency.py create mode 100644 pymcadre/prune/check_salvage_path.py create mode 100644 pymcadre/prune/find_inactive_rxns.py create mode 100644 pymcadre/prune/prune_model.py create mode 100644 pymcadre/rank/__init__.py create mode 100644 pymcadre/rank/calc_conn_evidence.py create mode 100644 pymcadre/rank/calc_expr_evidence.py create mode 100644 pymcadre/rank/initialize_generic_model.py create mode 100644 pymcadre/rank/map_gene_scores_to_rxns.py create mode 100644 pymcadre/rank/map_high_conf_to_rxns.py create mode 100644 pymcadre/rank/parse_gprs.py create mode 100644 pymcadre/rank/rank_reactions.py create mode 100644 pymcadre/test_scripts/python_recon1_with_BOF_and_VBOF__BEC1_method2.ipynb create mode 100644 pymcadre/test_scripts/test_check_model_consistency_module.ipynb create mode 100644 pymcadre/test_scripts/test_check_module.ipynb create mode 100644 pymcadre/test_scripts/test_prune_model_fastcc.ipynb create mode 100644 pymcadre/test_scripts/test_prune_module_fastFVA.ipynb create mode 100644 pymcadre/test_scripts/test_rank_reactions_module.ipynb diff --git a/pymcadre/__init__.py b/pymcadre/__init__.py new file mode 100644 index 0000000..d62c620 --- /dev/null +++ b/pymcadre/__init__.py @@ -0,0 +1,2 @@ +__author__ = "Nantia Leonidou" +__description__ = " " \ No newline at end of file diff --git a/pymcadre/check/__init__.py b/pymcadre/check/__init__.py new file mode 100644 index 0000000..d62c620 --- /dev/null +++ b/pymcadre/check/__init__.py @@ -0,0 +1,2 @@ +__author__ = "Nantia Leonidou" +__description__ = " " \ No newline at end of file diff --git a/pymcadre/check/check_model_function.py b/pymcadre/check/check_model_function.py new file mode 100644 index 0000000..c8fa636 --- /dev/null +++ b/pymcadre/check/check_model_function.py @@ -0,0 +1,115 @@ +__author__ = "Nantia Leonidou" +__description__ = """ Check production of required metabolites """ + +from time import process_time +from check.find_ex_reactions import * +from check.set_metabolite_bounds import * +from check.find_required_rxns import * +from check.check_rxn_flux import * +import os + + +def check_model_function(model, *args): + """ Check production of required metabolites + Inputs: - a cobra model + - optional inputs: - 'required_mets', met_lst + - 'biomass', biomass_rxn + - 'media', media_def + + Output: - required_met_status + - time """ + + ################################################################################################ + # Parse input parameters # + ################################################################################################ + if len(args) != 0: + if len(args) % 2 == 0: # if division between len(args) and 2 gives rest 0 + + options = ["required_mets", "biomass", "media"] + + for i in range(0, len(args), 2): # i goes from 1 to len(args) incrementally in steps of 2 + arg_name = args[i] # define arg_name, can be 'required_mets' or 'biomass' or 'media' + arg_val = args[i + 1] # define arg_val, can be met_lst or biomass_rxn or media_def + + # read input .txt file + with open(arg_val, 'r') as file: + # list of all input metabolites + met_lst = [line.rstrip('\n') for line in file] + + # set 1 if one of the options is given as arguments, else set 0 + option = [1 if arg_name == opt else 0 for opt in options] + + # find indices of nonzero elements in the lst, called options + # returns list with indices depending on whether an input argument from *args matches one of the strings in list 'options' + # Example: if 'media' is given as an argument in the check_model_function function, + # then the find_idx_option = [2], because the 'media' string is located in the index 2 in 'options' list + find_idx_option = [i for i, e in enumerate(option) if e != 0] + + # if indices of nonzero elements are found + # biomass_rxn = [] + # media_def = [] + if len(option) != 0: + for elem in find_idx_option: + if elem == 0: + arg_val = met_lst + elif elem == 1: + raise Exception("%s option not yet implemented." % arg_name) + # arg_val = biomass_rxn + elif elem == 2: + raise Exception("%s option not yet implemented." % arg_name) + # arg_val = media_def + # else-case + else: + raise Exception("Unknown option %s." % arg_name) + else: + raise Exception("Incorrect number of input arguments to function.", os.path.basename(__file__)) + ################################################################################################ + + # Start the stopwatch / counter + # returns float value of time in seconds + t1_start = process_time() + + # Identify exchange reactions in the model + ex_rxns = find_ex_rxns(model) + + # Turn off uptake of organic metabolites + if "media_def" in globals(): # check if variable named media_def is defined + set_media_ex_bounds(model, ex_rxns) # not implemented in this version + else: + set_organic_met_bounds(model, ex_rxns) + + # store reaction names + names = [] # rxn name + for r in model.reactions: + names.append(r.name) + + ########### + # Allow uptake of glucose and CO2, only if they are in the model + ########### + if 'D-Glucose exchange' in names: # Reaction id: EX_glc__D_e + idx = names.index('D-Glucose exchange') + model.reactions[idx].lower_bound = -5.0 + + if 'CO2 exchange' in names: # Reaction id: EX_co2_e + idx = names.index('CO2 exchange') + model.reactions[idx].lower_bound = -1000.0 + + # Add demand reactions for required metabolites + if "met_lst" in globals(): + model, required_rxns = find_required_rxns(model, met_lst) + else: + required_rxns = [] + + # if "biomass_rxn" in globals(): + # required_rxns = np.concatenate(required_rxns, biomass_rxn) # not implemented in this version + + inactive_required = check_rxn_flux(model, required_rxns) + required_met_status = int(not len(inactive_required)) # return negation of number corresponding to length of inactive_required list + + # Stop the stopwatch / counter + t1_stop = process_time() + # compute elapsed time + time = t1_stop - t1_start + + print('check_model_function done ....') + return required_met_status, time diff --git a/pymcadre/check/check_rxn_flux.py b/pymcadre/check/check_rxn_flux.py new file mode 100644 index 0000000..a93c0c1 --- /dev/null +++ b/pymcadre/check/check_rxn_flux.py @@ -0,0 +1,83 @@ +__author__ = "Nantia Leonidou" +__description__ = "This function uses the heuristic speed-up proposed by Jerby et al. in the MBA paper for performing a pseudo-FVA calculation. " + +# from cobra import * +# from check.find_required_rxns import * +import numpy as np + + +def check_rxn_flux(model, required_rxns): + """ + Input: + - model: cobra.io.core.model.Model + - required_rxns: list of required reactions to check their flux + + Output: + - inactive_required + """ + rxn_lst = required_rxns + inactive_required = [] + + while len(rxn_lst): # while lst is not empty + # set number of reactions equal to number of input reactions + num_rxn_lst = len(rxn_lst) + + # modify objective function + model.objective = rxn_lst + # optimize using glpk solver + fba_solution = model.optimize(objective_sense="maximize") + # get flux values of all reactions as an array + opt_max = fba_solution.fluxes.values + + # If no solution was achieved while trying to maximize all reactions, skip the next + # step of checking individual reactions + if len(opt_max) == 0: + inactive_required.append(1) + break # break the whole while-loop + + # check whether reactions from model are included in input required reactions + # put 1 if reaction from model is in the list of required reactions + is_member = [1 if react.id in required_rxns else 0 for react in model.reactions] + + # get fluxes for these specific reactions + required_flux = [opt_max[idx] for idx in range(len(is_member)) if is_member[idx]] + + # absolute values of all fluxes + abs_fluxes = [abs(ele) for ele in required_flux] + # filter out those with a specific value --> those reactions will be kept + filtered = [1 if abs_fluxes[idx] >= 1e-6 else 0 for idx in range(len(abs_fluxes))] + # get related reaction IDs + active_required = [required_rxns[idx] for idx in range(len(filtered)) if filtered[idx]] + + # update rxn_lst to be the difference between reactions' list and required active reactions + rxn_lst = (list(set(rxn_lst) - set(active_required))) + # get how many reactions were removed from required_rxns list --> updated length of rxns_lst + num_removed = num_rxn_lst - len(rxn_lst) + + if not num_removed: # if this if-case is fulfilled, throws an out-of-bounds error, similar happens to MATLAB code as well + # create a random series of numbers from 0 to len(rxn_lst) + rand_ind = np.random.permutation(len(rxn_lst)) + + # extract reaction from rxn_lst based on the position taken from the first number in the randomly generated series + i = rxn_lst[rand_ind[0]] + + # change objective function + model.objective = i + # Maximize reaction i + fba_solution = model.optimize(objective_sense="maximize") + # get flux values of all reactions + opt_max = fba_solution.fluxes + if len(opt_max) == 0: + inactive_required.append(i) + break # break the whole while-loop + + abs_opt = [abs(ele) for ele in opt_max] + for n in abs_opt: + if n < 1e-6: + inactive_required.append(i) + break + + rxn_lst.remove(i) + + return inactive_required + diff --git a/pymcadre/check/find_ex_reactions.py b/pymcadre/check/find_ex_reactions.py new file mode 100644 index 0000000..fde516c --- /dev/null +++ b/pymcadre/check/find_ex_reactions.py @@ -0,0 +1,26 @@ +__author__ = "Nantia Leonidou" +__description__ = " Identification of all exchange reactions in a given Cobra model" + + +from cobra import * + + +def find_ex_rxns(model): + + """ This function identifies reactions that exchange metabolites into and out of the extra- and intracellular space + (sinks, demands and exchanges) + + Input: + - model: cobra.io.core.model.Model + + Ouput: + - ex_rxns_ids: list of all identified reactions' IDs """ + + ex_rxns_ids = [] + + for react in model.reactions: + + if len(react.metabolites) == 1: + ex_rxns_ids.append(react.id) + + return ex_rxns_ids diff --git a/pymcadre/check/find_organic_ex_rxns.py b/pymcadre/check/find_organic_ex_rxns.py new file mode 100644 index 0000000..10f5f02 --- /dev/null +++ b/pymcadre/check/find_organic_ex_rxns.py @@ -0,0 +1,45 @@ +__author__ = "Nantia Leonidou" +__description__ = """ Detection of all organic reactions given a cobra model and a list of exchange reactions + (sink, demand and exchange reactions) """ + + +# from cobra import * +# from cobra.io.sbml import * +# from check.find_ex_reactions import * + +def find_organic_ex_rxns(model, ex_rxns): + """ Detection of organic reactions included in all exchange reactions + + Input: + - model: cobra.io.core.model.Model + - ex_rxns: list of reaction IDs + + Output: + - organic_ex_rxns: list of organic reactions' IDs""" + + # Organic metabolites contain carbon (C) and hydrogen (H) Thus, check molecular formulae + organic_metabolites = [] + for met in model.metabolites: + if "C" in met.formula and "H" in met.formula: + organic_metabolites.append(met.id) + else: + # add metabolites, that are organic but don't contain only "C" and "H" in their chemical formulae OR include protein compounds + if ("C" in met.formula and "R" in met.formula) or ("X" in met.formula and "H" in met.formula) \ + or ("C" in met.formula and "X" in met.formula) or ("H" in met.formula and "R" in met.formula): + organic_metabolites.append(met.id) + + # Find all organic reactions (i.e reactions evolving organic metabolites) + all_organic_reactions = [] + for met in organic_metabolites: + # all organic reactions associated with current organic metabolite + org_rxns = model.metabolites.get_by_id(met).reactions + for react in org_rxns: + # put all of them in a list, after excluding reactions that may come up multiple times + if react.id not in all_organic_reactions: + all_organic_reactions.append(react.id) + + # extract all exchange reactions that involve organic metabolites + # organic_ex_rxns = [react for react in ex_rxns if react in all_organic_reactions] + organic_ex_rxns = list(set(all_organic_reactions) & set(ex_rxns)) + + return organic_ex_rxns diff --git a/pymcadre/check/find_required_rxns.py b/pymcadre/check/find_required_rxns.py new file mode 100644 index 0000000..f8ad1c1 --- /dev/null +++ b/pymcadre/check/find_required_rxns.py @@ -0,0 +1,70 @@ +__author__ = "Nantia Leonidou" +__description__ = " Detect required reactions and add them to the model" + +from cobra import * + + +def add_metabolites(met_id_lst, coeffs_lst, compartment_lst): + """ Create a dictionary with metabolites and their coefficients + Input: lst with metabolites' IDs, list with repsective coefficients + and lst with respective compartment letters + Output: dictionary with metabolites""" + + if len(met_id_lst) != len(coeffs_lst) or len(met_id_lst) != len(compartment_lst) or len(coeffs_lst) != len( + coeffs_lst): + print("ERROR: Input lists should have the same size") + else: + met_dict = {} + for i in range(len(met_id_lst)): + met_dict[Metabolite(met_id_lst[i], compartment=compartment_lst[i])] = coeffs_lst[i] + return met_dict + + +def add_single_reaction(model, id, lb, up, met_dict): + """ Add reactions to a model. + Input: model, reaction id, lower/upper bound and dictionary with the metabolites to add + Output: model with a newly added reaction and the respective reaction.""" + + react = Reaction() + react.id = id + react.lower_bound, react.upper_bound = lb, up + # add metabolites by hand in the model, First checks whether the metabolites exist in the model + react.add_metabolites(met_dict) + + return model, react + + +def find_required_rxns(model, metabolites): + """ Input: model and list of metabollites in a .txt format (see example metabolites_humanModel.txt) + Output: model and list of only required reactions' id """ + + # define manually _coa metabolites + coa_mets = ['accoa_m', 'succoa_m', 'pmtcoa_c'] + + # read input file including diverse metabolites + with open(metabolites, 'r') as file: + # list of all input metabolites + met_lst = [line.rstrip('\n') for line in file] + + # difference between coa_mets and input list of metabolites --> list of strings + diff = (list(set(met_lst) - set(coa_mets))) + print(diff) + + required_rxns = [] + # add metabolites from diff as demand reactions, if metabolite is in the model + model_mets = [m.id for m in model.metabolites] + for met in diff: + r = model.add_boundary(model.metabolites.get_by_id(met),type="demand") # add_boundary if metabolite is already in the model + required_rxns.append(r.id) + + + react1 = add_single_reaction(model, "DM_accoa_m", 0.0,1000.0, met_dict={Metabolite('accoa_m', compartment='m'): -1, Metabolite('coa_m', compartment='m'): 1})[1] + required_rxns.append(react1.id) + react2 = add_single_reaction(model, "DM_succoa_m", 0.0,1000.0, met_dict={Metabolite('succoa_m', compartment='m'): -1, Metabolite('coa_m', compartment='m'): 1})[1] + required_rxns.append(react2.id) + react3 = add_single_reaction(model, "DM_pmtcoa_c", 0.0,1000, met_dict={Metabolite('pmtcoa_c', compartment='c'): -1, Metabolite('coa_c', compartment='c'): 1})[1] + required_rxns.append(react3.id) + model.add_reactions([react1,react2,react3]) + + return model, required_rxns + diff --git a/pymcadre/check/set_metabolite_bounds.py b/pymcadre/check/set_metabolite_bounds.py new file mode 100644 index 0000000..e6e2d9f --- /dev/null +++ b/pymcadre/check/set_metabolite_bounds.py @@ -0,0 +1,40 @@ +__author__ = "Nantia Leonidou" +__description__ = " Modify metabolites' bounds " + +from check.find_organic_ex_rxns import * + + +def set_organic_met_bounds(model, ex_rxns): + """ Set lower bound of organic reactions to 0.0, aiming the turn-off of the uptake + + Input: a cobra model and a list of reaction IDs + + Output: a cobra model with the updated bounds """ + + # Identify all exchange reactions that include organic metabolites + organic_ex_rxns = find_organic_ex_rxns(model, ex_rxns) + + # Reset all lower bounds for organic reactions to 0 to disable uptake + for react in organic_ex_rxns: + model.reactions.get_by_id(react).lower_bound = 0.0 + + ############# + # check whether bounds were set to 0.0 + # for r in organic_ex_rxns: + # print(model.reactions.get_by_id(r).bounds) + ############ + + return model + + +############################################################################## +# not implemented in this version --> see MATLAB code +def set_media_ex_bounds(model, ex_rxns): + # for rxns in ex_rxns: + # + # # set all lower and upper bounds to 0 + # model.reactions.get_by_id(rxns).lower_bound = 0.0 + # model.reactions.get_by_id(rxns).upper_bound = 0.0 + print("Not implemented yet.") + return model +############################################################################### diff --git a/pymcadre/code_organization.txt b/pymcadre/code_organization.txt new file mode 100644 index 0000000..8452ec3 --- /dev/null +++ b/pymcadre/code_organization.txt @@ -0,0 +1,32 @@ +# Dependency tree for mcadre modules/functions + +pymcadre/ # main pymcadre function +|-----rank_reactions/ + |-------------parse_gprs + |-------------map_high_conf_to_rxns + |-------------map_gene_scores_to_rxns + |-------------calc_expr_evidence + |-------------initialize_generic_model + |-----------------------check_model_consistency [see below] + |-------------calc_conn_evidence +|-----check_model_function [see below] +|-----prune_model/ + |----------check_model_function [see below] + |----------check_salvage_path [see below] + |----------check_model_consistency [see below] + +core_functions/ # recurring internal functions +|-------------check_model_function/ # checks production of req. metabolites + |-------------------find_ex_rxns + |-------------------set_metabolite_bounds + |-----------------find_organic_ex_rxns + |-------------------find_required_rxns + |-------------------check_rxn_flux +|-------------check_salvage_path/ # checks for nucleotide salvage + |-----------------find_ex_reactions + |-----------------set_metabolite_bounds +|-------------check_model_consistency/ # checks for inactive reactions + |----------------------check_core_deadends + |----------------------find_inactive_rxns + |-----------------fastFVA + |-----------------fastcc diff --git a/pymcadre/main_pymcadre.ipynb b/pymcadre/main_pymcadre.ipynb new file mode 100644 index 0000000..c016a3a --- /dev/null +++ b/pymcadre/main_pymcadre.ipynb @@ -0,0 +1,214 @@ +{ + "cells": [ + { + "cell_type": "code", + "source": [ + "__author__ = \"Nantia Leonidou\"\n", + "__description__ = \" Run pymCADRE \"\n", + "\n", + "from rank.rank_reactions import *\n", + "from prune.prune_model import *" + ], + "outputs": [], + "execution_count": null, + "metadata": {} + }, + { + "cell_type": "markdown", + "source": [ + "\n", + " Inputs:\n", + " - model: original generic model\n", + " - precursorMets: name of .txt file with precursor metabolites as string\n", + " - G: list of genes in expression data\n", + " - U: ubiquity scores corresponding to genes in G\n", + " - confidenceScores: literature-based evidence for generic model reactions\n", + " - salvageCheck: option flag for whether to perform functional check for the\n", + " nucleotide salvage pathway (1) or not (0)\n", + " - C_H_genes: predefined high confidence reactions (optional)\n", + " - method: 1 = use fastFVA (glpk) to check consistency; 2 = use fastcc & cplex\n", + "\n", + " Outputs:\n", + " - PM: pruned, context-specific model\n", + " - GM: generic model (after removing blocked reactions)\n", + " - C: core reactions in GM\n", + " - NC: non-core reactions in GM\n", + " - Z: reactions with zero expression (i.e., measured zero, not just\n", + " missing from expression data)\n", + " - model_C: core reactions in the original model (including blocked)\n", + " - pruneTime: total reaction pruning time\n", + " - cRes: result of model checks (consistency/function)\n", + " - vs. +: reaction r removed from generic model or not\n", + " 1 vs. 2: reaction r had zero or non-zero expression evidence\n", + " -x.y: removal of reaction r corresponded with removal of y (num.) total core reactions\n", + " +x.1 vs. x.0: precursor production possible after removal of reaction r or not\n", + " 3: removal of reaction r by itself prevented production of required metabolites (therefore was not removed) \n" + ], + "metadata": {} + }, + { + "cell_type": "markdown", + "source": [ + "## Import Sample Dataset" + ], + "metadata": {} + }, + { + "cell_type": "code", + "source": [ + "# read model\n", + "model = io.read_sbml_model('../test_dataset/recon1_with_BOF_and_VBOF.xml')\n", + "# genes\n", + "G = pd.read_csv('../test_dataset/1_GPL570_GSE3397_entrez_ids.csv')\n", + "G = list(G['ENTREZ_GENE_ID'])\n", + "# ubiquity scores\n", + "U = pd.read_csv('../test_dataset/1_GPL570_GSE3397_ubiquity.csv', header=None)\n", + "U = U.rename(columns={0: \"Scores\"})\n", + "U = list(U['Scores'])\n", + "#confidence_scores\n", + "#confidence_scores = get_test_inputs('../testInputs.mat','../humanModel.mat')[3]\n", + "#confidence_scores[-1] = 4\n", + "confidence_scores = pd.read_csv('../test_dataset/Recon1_confidence_scores_with_BOF_and_VBOF.csv')\n", + "confidence_scores = np.float64(list(confidence_scores['Confidence Score']))" + ], + "outputs": [], + "execution_count": null, + "metadata": {} + }, + { + "cell_type": "markdown", + "source": [ + "## Ranking" + ], + "metadata": {} + }, + { + "cell_type": "code", + "source": [ + "##############################################\n", + "# Rank reactions\n", + "##############################################\n", + "\n", + "print('Processing inputs and ranking reactions...')\n", + "GM, C, NC, P, Z, model_C = rank_reactions(model, G, U, confidence_scores, [], 1)" + ], + "outputs": [], + "execution_count": null, + "metadata": {} + }, + { + "cell_type": "code", + "source": [ + "print(len(GM.reactions),len(GM.metabolites),len(GM.genes),len(C),len(NC),len(Z),len(model_C))" + ], + "outputs": [], + "execution_count": null, + "metadata": {} + }, + { + "cell_type": "markdown", + "source": [ + "## Check model consistency" + ], + "metadata": {} + }, + { + "cell_type": "code", + "source": [ + "##################################################\n", + "# Define inputs to the model pruning step\n", + "##################################################\n", + "# Define core vs. non-core ratio threshold for removing reactions\n", + "eta = 1 / 3\n", + "# Check functionality of generic model\n", + "genericStatus = check_model_function(GM, 'required_mets', precursorMets)[0]" + ], + "outputs": [], + "execution_count": null, + "metadata": {} + }, + { + "cell_type": "markdown", + "source": [ + "## Pruning" + ], + "metadata": {} + }, + { + "cell_type": "code", + "source": [ + "if genericStatus:\n", + " print('Generic model passed precursor metabolites test')\n", + "\n", + " ##############################################################\n", + " # If generic functionality test is passed, prune reactions\n", + " ###############################################################\n", + " print('Pruning reactions...')\n", + " t0 = process_time()\n", + " PM, cRes = prune_model(GM, P, C, Z, eta, '../test_dataset/key_metabolites_RECON1.txt', salvage_check=1, method=1)\n", + " # Stop the stopwatch / counter\n", + " t_stop = process_time()\n", + " # compute elapsed time\n", + " pruneTime = t_stop - t0\n", + "\n", + "else:\n", + " print('Generic model failed precursor metabolites test!!')" + ], + "outputs": [], + "execution_count": null, + "metadata": {} + }, + { + "cell_type": "code", + "source": [ + "print(len(PM.reactions),len(PM.metabolites),len(PM.genes),pruneTime)" + ], + "outputs": [], + "execution_count": null, + "metadata": {} + }, + { + "cell_type": "markdown", + "source": [ + "## Store pruned model" + ], + "metadata": {} + }, + { + "cell_type": "code", + "source": [ + "#########################################\n", + "# * store pruned model in SBML format *\n", + "#########################################\n", + "io.write_sbml_model(PM, \"pruned_model.xml\")" + ], + "outputs": [], + "execution_count": null, + "metadata": {} + } + ], + "metadata": { + "kernelspec": { + "name": "python3", + "language": "python", + "display_name": "Python 3 (built-in)" + }, + "language_info": { + "name": "python", + "version": "3.6.3", + "mimetype": "text/x-python", + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "pygments_lexer": "ipython3", + "nbconvert_exporter": "python", + "file_extension": ".py" + }, + "kernel_info": { + "name": "python3" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} \ No newline at end of file diff --git a/pymcadre/main_pymcadre.py b/pymcadre/main_pymcadre.py new file mode 100644 index 0000000..1f2daf8 --- /dev/null +++ b/pymcadre/main_pymcadre.py @@ -0,0 +1,66 @@ +__author__ = "Nantia Leonidou" +__description__ = " pymCADRE main" + +from time import process_time +from rank.rank_reactions import * +from prune.prune_model import * +import pandas as pd +import numpy as np +from cobra import * +from cobra.io.sbml import * + + +# read model +model = io.read_sbml_model('../test_dataset/recon1_with_BOF_and_VBOF.xml') +# genes +G = pd.read_csv('../test_dataset/1_GPL570_GSE3397_entrez_ids.csv') +G = list(G['ENTREZ_GENE_ID']) +# ubiquity scores +U = pd.read_csv('../test_dataset/1_GPL570_GSE3397_ubiquity.csv', header=None) +U = U.rename(columns={0: "Scores"}) +U = list(U['Scores']) +#confidence_scores +confidence_scores = pd.read_csv('../test_dataset/Recon1_confidence_scores_with_BOF_and_VBOF.csv') +confidence_scores = np.float64(list(confidence_scores['Confidence Score'])) + +############################################## +# Rank reactions +############################################## + +print('Processing inputs and ranking reactions...') +GM, C, NC, P, Z, model_C = rank_reactions(model, G, U, confidence_scores, [], method=1) + +################################################## +# Define inputs to the model pruning step +################################################## +# Define core vs. non-core ratio threshold for removing reactions +eta = 1 / 3 +# Check functionality of generic model +genericStatus = check_model_function(deepcopy(GM), 'required_mets', '../test_dataset/key_metabolites_RECON1.txt')[0] + +if genericStatus: + print('Generic model passed precursor metabolites test') + + ############################################################## + # If generic functionality test is passed, prune reactions + ############################################################### + print('Pruning reactions...') + t0 = process_time() + PM, cRes = prune_model(GM, P, C, Z, eta, '../test_dataset/key_metabolites_RECON1.txt', salvage_check=1, method=1) + # Stop the stopwatch / counter + t_stop = process_time() + # compute elapsed time + pruneTime = t_stop - t0 + +else: + print('Generic model failed precursor metabolites test!!') + +print('PM.reactions: ',len(PM.reactions)) +print('PM.metabolites: ',len(PM.metabolites)) +print('PM.genes: ', len(PM.genes)) +print('prune Time: ', pruneTime) + +######################################### +# * store pruned model in SBML format * +######################################### +io.write_sbml_model(PM, "python_recon1_BEC1_method1.xml") diff --git a/pymcadre/prune/__init__.py b/pymcadre/prune/__init__.py new file mode 100644 index 0000000..d62c620 --- /dev/null +++ b/pymcadre/prune/__init__.py @@ -0,0 +1,2 @@ +__author__ = "Nantia Leonidou" +__description__ = " " \ No newline at end of file diff --git a/pymcadre/prune/check_core_deadends.py b/pymcadre/prune/check_core_deadends.py new file mode 100644 index 0000000..1ba3961 --- /dev/null +++ b/pymcadre/prune/check_core_deadends.py @@ -0,0 +1,93 @@ +__author__ = "Nantia Leonidou" +__description__ = " " + +from cobra import * +import numpy as np + + +def is_member(A, B): + """ Check which elements from A are also in B """ + check = [] + for a in A: + if a in B: + check.append(1) + else: + check.append(0) + return check + + +def check_core_dead_ends(model, core_rxns): + """ Input: + - model + - core_rxns: list of core reactions + + Output: + - dead_end_core_rxns: list of dead-end core reactions""" + + # create stoichiometric matrix + # --> S[i,j] contains the quantity of metabolite i produced (negative for consumed) by reaction j + s_matrix = util.array.create_stoichiometric_matrix(model) + + rev = [] # get reversibility of all reactions + for react in model.reactions: + r_id = react.id + rev.append(model.reactions.get_by_id(r_id).reversibility) + + dead_end_core_rxns = [] + for met in range(len(model.metabolites)): + de_mets = 0 + + both_rxns = [] + for i in range(len(s_matrix[met, :])): # iterate over selected row (based on met) in stoichiometric matrix + if (s_matrix[met, :][i] != 0) and ( + rev[i]): # find all non-zero values in current row and those reactions that are reversible + both_rxns.append(i) # store column index, when above criterion is fulfilled + + pos_rxns = [] # produced reactions + for i in range(len(s_matrix[met, :])): # iterate over selected row (based on met) in stoichiometric matrix + if s_matrix[met, :][i] > 0: + pos_rxns.append(i) + # union of both lists + produced_rxns = list(set(pos_rxns) | set(both_rxns)) + # print("produced",len(produced_rxns),produced_rxns) + + neg_rxns = [] # consumed reactions + for i in range(len(s_matrix[met, :])): # iterate over selected row (based on met) in stoichiometric matrix + if s_matrix[met, :][i] < 0: + neg_rxns.append(i) + # union of both lists + consumed_rxns = list(set(neg_rxns) | set(both_rxns)) + # print("consumed",len(consumed_rxns), consumed_rxns) + + # Check for produced-only metabolites + if len(consumed_rxns) == 0: + # dead-ends: 1 if dead-ends were found, otherwise 0 + de_mets = 1 + # Check for consumed-only metabolites + elif len(produced_rxns) == 0: + de_mets = 1 + # Check for metabolites both consumed and produced, but only in a single + # reversible reaction + else: + if (len(produced_rxns) == 1) and (len(consumed_rxns) == 1) and (produced_rxns == consumed_rxns): + de_mets = 1 + # print(de_mets) + + # If dead end found => check for overlap with core reactions + # If any core reaction contains a dead-end metabolite => the reaction itself will be a dead end. + # This check avoids subsequent optimizations, as the function terminates if any blocked core reactions are detected. + if de_mets == 1: + # store names of found dead-end reactions + is_de = [] + # iterate over current matrix row (current metabolite) + for i in range(len(s_matrix[met, :].astype(np.int64))): + if s_matrix[met, :].astype(np.int64)[i] == 1 or s_matrix[met, :].astype(np.int64)[i] == -1: + is_de.append(model.reactions[i].id) + # print(is_de,len(is_de)) + + # check whether detected dead-ends are core reactions as well + if any(is_member(is_de, core_rxns)): + dead_end_core_rxns = is_de + break + + return dead_end_core_rxns diff --git a/pymcadre/prune/check_model_consistency.py b/pymcadre/prune/check_model_consistency.py new file mode 100644 index 0000000..515d930 --- /dev/null +++ b/pymcadre/prune/check_model_consistency.py @@ -0,0 +1,82 @@ +__author__ = "Nantia Leonidou" +__description__ = " Check a model's consistency by identifying inactive (dead-end) reactions" + +from time import process_time +from cobra.flux_analysis import * +from prune.check_core_deadends import * +from prune.find_inactive_rxns import * + + +def check_model_consistency(model, method=1, rxn_to_remove=[], de_check=0, core_rxns=[]): + """ Identification of dead-end reactions in a stoichiometric model. + The function operates either independently to detect inactive reactions + for a model, or within a pruning algorithm (e.g., MBA) to study the + effect of removing reactions. + It is mainly based on a heuristic speed-up version of the Flux Variability + Analysis (FVA) proposed by (Jerby et al., 2010) + + Inputs: + - model: COBRA model structure + optional inputs: + - method: either fastFVA (1) or fastcc (2) + - rxn_to_remove: name of reaction to be removed (for model pruning in mCADRE or MBA) + - de_check: check for core reactions containing dead end metabolites + (only for use with model pruning in MBA) + - core_rxns: list of core reaction names (only for model pruning in MBA) + + Outputs: + - inactive_rxns: list of IDs corresponding to reactions with 0 mininum and 0 maximum flux + - time: CPU time required to complete function + - result: summary indicator of dead-end effects on inactive reactions. If + result = 1: removal of rxn_to_remove * DID NOT * create metabolite dead ends leading + to inactivation of core reactions + result = 2: removal of rxn_to_remove created metabolite dead ends leading to + inactivation of core reactions""" + + if len(rxn_to_remove): + model.remove_reactions(rxn_to_remove, remove_orphans=True) + + # set all objective coefficients to 0 + for react in range(len(model.reactions)): + model.reactions[react].objective_coefficient = 0 + + inactive_rxns = rxn_to_remove + + t1_start = process_time() + result = 1 # (until proven otherwise) assume removal or rxn_to_remove does not create any dead-end metabolite + + ################################################################################### + # check whether any core reactions are blocked by the removal of rxn_to_remove + ################################################################################### + # A core reaction is considered to be dead-end , if it contains a dead-end metabolite. + # Function exits if any blocked core reactions are detected. + if de_check: + dead_end_cores = check_core_dead_ends(model, core_rxns) + else: + dead_end_cores = [] + + # If no core reactions are blocked based on metabolite dead + # ends, maximize and minimize reactions to get those with zero flux + # capacity. + if len(dead_end_cores): + # Setting inactive_rxns to include dead-end-containing reactions will + # effectively cause the function to exit without checking non-core + # reactions below; thus, the full list of inactive reactions will not + # be enumerated + inactive_rxns = list(set(dead_end_cores) | set(inactive_rxns)) + + # indicates that dead-end-containing reactions were found in the core + result = 2 + + else: + # Otherwise, fastFVA is used to quickly scan through all + # reactions. **note: may want to include option to use fastFVA with GLPK + fast_scan = find_inactive_rxns(model, method) + inactive_rxns = list(set(inactive_rxns) | set(fast_scan)) + + t1_stop = process_time() + exec_time = t1_stop - t1_start + print('Execution time of check_model_consistency: %s s' % exec_time) + print('check_model_consistency done ... ') + + return inactive_rxns, exec_time, result diff --git a/pymcadre/prune/check_salvage_path.py b/pymcadre/prune/check_salvage_path.py new file mode 100644 index 0000000..d66fed7 --- /dev/null +++ b/pymcadre/prune/check_salvage_path.py @@ -0,0 +1,103 @@ +__author__ = "Nantia Leonidou" +__description__ = " Check the salvage pathway. " \ + " Test the ability of all tissues to synthesize purine nucleotides from purines bases and PRPP, " \ + " as de novo purine synthesis occurs primarily in the liver and other tissues uses salvage pathway." + +from cobra import * +from check.find_ex_reactions import * +from check.set_metabolite_bounds import * +from time import process_time + + +def check_salvage_path(model): + """ * not useful for tissues known to make purines de novo * + When the model is allowed to use PRPP and guanine or hypoxanthine, test if it + can make GMP or IMP. This is the salvage pathway that non-hepatic tissues use + for purine synthesis. + + Input: + - model: cobra.io.core.model.Model + + Output: + - salvage_status and time of execution""" + + t1_start = process_time() + + # find exchange reactions in the model + ex_rxns = find_ex_rxns(model) + + # turn off uptake of organic metabolites + if "media_def" in globals(): # check if variable named media_def is defined + model = set_media_ex_bounds(model, ex_rxns) # not implemented in this version + else: + model = set_organic_met_bounds(model, ex_rxns) + + # add PRPP sink reaction for subsequent checks + try: + model.metabolites.get_by_id("prpp_c") + model.add_boundary(model.metabolites.get_by_id("prpp_c"), type="sink", lb=-5, ub=5) + except: + met_lst = [Metabolite("prpp_c", compartment='c')] + model.add_metabolites(met_lst) + model.add_boundary(model.metabolites.get_by_id("prpp_c"), type="sink", lb=-5, ub=5) + + # store reaction names + names = [] # rxn name + for r in model.reactions: + names.append(r.name) + + ############################## + # Check production of GMP: + ############################## + # allow uptake of guanine + model_gmp = model.copy() + if "Guanine exchange" in names: # Reaction id: EX_gua_e + idx = names.index("Guanine exchange") + model_gmp.reactions[idx].lower_bound = -5.0 + # add demand reaction for GMP + try: + model_gmp.metabolites.get_by_id("gmp_c") + gmp_react = model_gmp.add_boundary(model_gmp.metabolites.get_by_id("gmp_c"), type="demand") + except: + met_lst = [Metabolite("gmp_c", compartment='c')] + model_gmp.add_metabolites(met_lst) + gmp_react = model_gmp.add_boundary(model_gmp.metabolites.get_by_id("gmp_c"), type="demand") + # modify objective function + model_gmp.objective = {gmp_react: 1} + # optimize using glpk solver + sol = model_gmp.optimize(objective_sense="maximize") + # True or False if objective value is greater than 1e-6 + status_gmp = sol.objective_value > 1e-6 + + ############################## + # Check production of IMP: + ############################## + # allow uptake of hypoxanthine + model_imp = model.copy() + if "Hypoxanthine exchange" in names: # Reaction id: EX_hxan_e + idx = names.index("Hypoxanthine exchange") + model_imp.reactions[idx].lower_bound = -5.0 + # add demand reaction for IMP + try: + model_imp.metabolites.get_by_id("imp_c") + imp_react = model_imp.add_boundary(model_imp.metabolites.get_by_id("imp_c"), type="demand") + except: + met_lst = [Metabolite("imp_c", compartment='c')] + model_imp.add_metabolites(met_lst) + imp_react = model_imp.add_boundary(model_imp.metabolites.get_by_id("imp_c"), type="demand") + # modify objective function + model_imp.objective = {imp_react: 1} + # optimize using glpk solver + sol = model_imp.optimize(objective_sense="maximize") + # True or False if objective value is greater than 1e-6 + status_imp = sol.objective_value > 1e-6 + + # get final salvage status + salvage_status = status_gmp & status_imp + + # Stop the stopwatch / counter + t1_stop = process_time() + # compute elapsed time + time = t1_stop - t1_start + + return salvage_status, time diff --git a/pymcadre/prune/find_inactive_rxns.py b/pymcadre/prune/find_inactive_rxns.py new file mode 100644 index 0000000..060350f --- /dev/null +++ b/pymcadre/prune/find_inactive_rxns.py @@ -0,0 +1,69 @@ +__author__ = "Nantia Leonidou" +__description__ = " Detect inactive reactions using either fastFVA oder FASTCC " + +from cobra.flux_analysis import flux_variability_analysis, fastcc +from cobra.flux_analysis import find_blocked_reactions +# from cobra import * +# from cobra.io.sbml import * + + +def find_inactive_rxns(model, method=1): + """ ** Runnable only in jupyter notebook ** + Find all inactive (blocked) reactions in a cobra model using either fastFVA or FASTCC methods + + Input: + - model: cobra.io.core.model.Model + - method: fastFVA(1, default) or FASTCC (2) + + Output: + - inactive_rxns: list of inactive reactions """ + + # inactive_rxns = [] + if method == 1: # fastFVA (by default, if no method number is given) + + print("Checking all reactions (fastFVA)...") + # set all objective coefficients to 0 + for react in range(len(model.reactions)): + model.reactions[react].objective_coefficient = 0 + + inactive_rxns = find_blocked_reactions(model) + ##################################################################################### + # ** ALTERNATIVELY: ** + # following code delivers the same inactive reactions as find_blocked_reactions + ##################################################################################### + # conduct FVA analysis + #fva = flux_variability_analysis(model) # add number of allowed tasks (threads) to run at the same time + #print("FVA is done...") + # store all maximum and all minimum flux-values after FVA + #opt_max = [] + #opt_min = [] + #for i in range(len(fva)): + # opt_max.append(fva.iloc[i][1]) + # opt_min.append(fva.iloc[i][0]) + #print("storing done...") + # set constraints to consider a reaction "inactive" + #abs_max = [i for i in range(len(opt_max)) if abs(opt_max[i]) < 1e-6] + #abs_min = [i for i in range(len(opt_min)) if abs(opt_min[i]) < 1e-6] + #print("Constraints done..") + #is_inactive = [rxn_id for rxn_id in abs_max if rxn_id in abs_min] + # get all (inactive) blocked reactions' id + #inactive_rxns = [] + #for rxn_id in is_inactive: + # inactive_rxns.append(model.reactions[rxn_id].id) + ######################################################################### + + else: # otherwise use FASTCC + + print("Checking all reactions (FASTCC)...") + # get non-blocked reactions, * in MATLAB the fastcc function gives less is_active reactions * + is_active = fastcc(model, zero_cutoff=1e-4).reactions + # get all active reactions' id + active_rxns = [rxn.id for rxn in is_active] + # get all model's reactions + all_model_rxns = [rxns.id for rxns in model.reactions] + # get difference, which are then the inactive reactions + inactive_rxns = list(set(all_model_rxns) - set(active_rxns)) + + print('Model consists of %s blocked (inactive) reactions' % len(inactive_rxns)) + return inactive_rxns + diff --git a/pymcadre/prune/prune_model.py b/pymcadre/prune/prune_model.py new file mode 100644 index 0000000..84da021 --- /dev/null +++ b/pymcadre/prune/prune_model.py @@ -0,0 +1,163 @@ +__author__ = "Nantia Leonidou" +__description__ = " Prune Model " + +from check.check_model_function import * +from prune.check_salvage_path import * +from prune.check_model_consistency import * +import numpy as np + + +def prune_model(GM, P, C, Z, eta, precursor_mets, salvage_check=1, method=1, cutoff=np.inf): + # default salvage_check value is 1 --> assume non-hepatic tissue, where nucleotides are not expected to be produced de novo + + # Initialize variables + R_G = [r.id for r in GM.reactions] + PM = GM + R_P = R_G + + NC_removed = 0 + C_removed = 0 + cRes = [0] * 3000 + count = 1 + + while len(P) != 0 and count < cutoff: + print('Reaction no. ', count) + r = P[0] + print('Attempting to remove reaction: ', r, '...') + print('Initial PM reactions:', len(PM.reactions)) + modelR = PM.copy() + modelR.remove_reactions([r], remove_orphans=True) + + # First check precursor production; + # if this test fails, no need to check model consistency with FVA (time-saving step) + rStatus = check_model_function(modelR, 'required_mets', precursor_mets)[0] + + # If specified, check the salvage pathway as well + if salvage_check: + rSalvage = check_salvage_path(modelR)[0] + rStatus = rStatus and rSalvage + + if rStatus: + # Check for inactive reactions after removal of r using a copy of PM + copyPM = PM.copy() + inactive_G = sorted(check_model_consistency(copyPM, method, [r])[0]) # get inactive reactions, includes a remove command + + inactive_C = list(set(inactive_G) & set(C)) + inactive_NC = list(set(inactive_G) - set(inactive_C)) + print('Lengths all--> inactive_G: %s , inactive_C: %s, inactive_NC:%s' %(len(inactive_G), inactive_C, inactive_NC)) + + # Remove reactions with zero expression (previously penalized in + # rank_reactions) and corresponding inactive core reactions, only if + # sufficiently more non-core reactions are removed + if r in Z: + print('Zero-expression evidence for reaction...') + # Check model function with all inactive reactions removed + modelTmp = PM.copy() + modelTmp.remove_reactions(inactive_G,remove_orphans=True) + tmpStatus = check_model_function(modelTmp, 'required_mets', precursor_mets)[0] + + # If specified, check the salvage pathway as well + if salvage_check: + tmpSalvage = check_salvage_path(modelTmp)[0] + tmpStatus = tmpStatus and tmpSalvage + + if (len(inactive_C) / len(inactive_NC) <= eta) and tmpStatus: + R_P_ids = [item.id for item in GM.reactions] + R_P = sorted(list(set(R_P_ids) - set(inactive_G))) + + PM.remove_reactions(inactive_G,remove_orphans=True) + + for i in inactive_G: + if i in P: + P.remove(i) + NC_removed = NC_removed + len(inactive_NC) + C_removed = C_removed + len(inactive_C) + num_removed = NC_removed + C_removed + print('Removed all inactive reactions') + + # result = -1.x --> reaction r had zero expression evidence and was removed along with any + # consequently inactivated reactions; + # x indicates the number of core reactions removed + if len(inactive_C) > 100: + removed_C_indicator = len(inactive_C) / 100 + else: + removed_C_indicator = len(inactive_C) / 10 + result = -1 - removed_C_indicator + + else: + # no reactions (core or otherwise) are actually + # removed in this step, but it is necessary to update the + # total number of removed reactions to avoid errors below + num_removed = NC_removed + C_removed + P.pop(0) + print('No reactions removed') + + # result = 1.x --> no reactions were removed because removal of r either led to a ratio + # of inactivated core vs. non-core reactions above the specified threshold + # eta (x = 1) or the removal of r and consequently inactivated reactions prevented + # production of required metabolites (x = 0) + result = 1 + tmpStatus / 10 + + # If reaction has expression evidence, only attempt to remove + # inactive non-core reactions + else: + print('Reaction %s is not in Z' %(r)) + # when r is not in Z + # Check model function with non-core inactive reactions removed + modelTmp = PM.copy() + modelTmp.remove_reactions(inactive_NC, remove_orphans=True) + tmpStatus = check_model_function(modelTmp, 'required_mets', precursor_mets)[0] + + # If specified, check the salvage pathway as well + if salvage_check: + tmpSalvage = check_salvage_path(modelTmp)[0] + tmpStatus = tmpStatus and tmpSalvage + + if (len(inactive_C) == 0) and tmpStatus: + R_P_ids = [item.id for item in GM.reactions] + R_P = sorted(list(set(R_P_ids) - set(inactive_NC))) + PM.remove_reactions(inactive_NC, remove_orphans=True) + for i in inactive_G: + if i in P: + P.remove(i) + NC_removed = NC_removed + len(inactive_NC) + num_removed = NC_removed + C_removed + print('Removed non-core inactive reactions') + + # result = -2.x --> reaction r had expression + # evidence and was removed along with (only) non-core inactivated reactions; + # x indicates the number of core reactions removed (should be zero!) + if len(inactive_C) > 100: + removed_C_indicator = len(inactive_C) / 100 + else: + removed_C_indicator = len(inactive_C) / 10 + + result = -2 - removed_C_indicator + + else: + num_removed = NC_removed + C_removed + P.pop(0) + print('No reactions removed') + + # result = 2.x --> no reactions were removed because removal of r either led to inactivated core + # reactions (x = 1) or the removal of r and consequently inactivated reactions prevented production + # of required metabolites (x = 0) + result = 2 + tmpStatus / 10 + + else: + num_removed = NC_removed + C_removed + P.pop(0) + + # result = 3 --> no reactions were removed because + # removal of r by itself prevented production of required metabolites + result = 3 + + cRes[count] = result + count += 1 + print('Num. removed: %s (%s core, %s non-core); Num. remaining: %s' % (num_removed, C_removed, NC_removed, len(P))) + + cRes[count:] = [] + print('prune_model done .... ') + return PM, cRes + + diff --git a/pymcadre/rank/__init__.py b/pymcadre/rank/__init__.py new file mode 100644 index 0000000..d62c620 --- /dev/null +++ b/pymcadre/rank/__init__.py @@ -0,0 +1,2 @@ +__author__ = "Nantia Leonidou" +__description__ = " " \ No newline at end of file diff --git a/pymcadre/rank/calc_conn_evidence.py b/pymcadre/rank/calc_conn_evidence.py new file mode 100644 index 0000000..f2c3e67 --- /dev/null +++ b/pymcadre/rank/calc_conn_evidence.py @@ -0,0 +1,50 @@ +__author__ = "Nantia Leonidou" +__description__ = " Calculate connectivity evidence " + +from cobra import * +import numpy as np + + +def calc_conn_evidence(model, E_X): + """ Input: + - model: cobra.io.core.model.Model --> GM model computed from initialize_generic_model + - E_X: list of E_X computed from initialize_generic_model + + Output: + - E_C: list of connectivity scores """ + + # create stoichiometric matrix + s_mtrx = util.array.create_stoichiometric_matrix(model) + # S matrix should be binarized to indicate metabolite participation in each reaction + S_bin = abs(s_mtrx.astype(np.int64)) + + # Adjacency matrix (i.e., binary reaction connectivity); the connection between + # a reaction and itself is ignored by subtracting the identity matrix + S_bin_transpose = np.transpose(S_bin) # transpose matrix S_bin + mult = S_bin_transpose.dot(S_bin) + for i in range(len(mult)): + for j in range(len(mult[i])): + if mult[i][j] != 0: + mult[i][j] = 1 + # subtract the identity matrix + id_mtrx = np.identity(S_bin.shape[1]) + # final Adjacency matrix + A = mult - id_mtrx + + # Influence matrix --> describes the divided connectivity of reactions -- + # e.g., if RXN1 is connected to 4 reactions, its influence on each of those reactions would be 0.25 + row_sum = np.sum(A, axis=1) # sum of elements in each row of matrix A + rep = np.array([row_sum, ] * A.shape[ + 0]).transpose() # construct an array by repeating column vector row_sum as many times as shape of matrix A + I = A / rep # define Influence Matrix + + # Weighted influence matrix --> each reaction's influence on others is weighted by its expression score. Thus, reactions with with 0 in the + # corresponding cell, have no weighted influence on adjacent reactions + rep2 = np.array([E_X, ] * A.shape[0]).transpose() + # element-wise multiplication + WI = np.multiply(rep2, I) + + # Connectivity score --> sum the influence of all connected reactions + E_C = np.nansum(WI,axis=0).tolist() + + return E_C diff --git a/pymcadre/rank/calc_expr_evidence.py b/pymcadre/rank/calc_expr_evidence.py new file mode 100644 index 0000000..c8dafdc --- /dev/null +++ b/pymcadre/rank/calc_expr_evidence.py @@ -0,0 +1,55 @@ +__author__ = "Nantia Leonidou" +__description__ = " Calculate expression-based evidence " + +# import numpy as np +# from cobra import * +# from rank.parse_gprs import * +# from rank.map_high_conf_to_rxns import * +# from rank.map_gene_scores_to_rxns import * +# from test_Inputs.test_Inputs import * +import math +import numpy as np + + +def calc_expr_evidence(model, GPR_rxns, U_GPR, is_C_H): + """ Compute expression-bsed evidence: function of how often genes, associated to a reaction, + is expressed in the selected context. E_X is ranged from 0 to 1 and its relation to + the ubiquity scores is a composite of the Boolean gene-reaction rules defined in the generic + model. + + Input: + - generic model --> cobra.io.core.model.Model + - GPR_rxns --> list of reaction IDs, obtained from GPRs, as strings + - U_GPR --> list of lists, with ubiquity scores as float numbers + - is_C_H --> list of 0 or 1 indicating high confidence or not + + Output: + - E_X --> list of respective expression-based evidence. If 0, then this reaction + has strong evidence of not being active in the respective tissue context""" + + # create list with zeros + E_X = [0.0] * len(model.reactions) + + # get minimum of each list in U_GPR(list of lists) + U_GPR_min = [np.nanmin(l) for l in U_GPR] + + all_rxns = [r.id for r in model.reactions] + + # find existence of model.reactions in the GPR_rxns list + for i in range(len(all_rxns)): + rxn_GPRS = [] # store indices, where a model reaction is found + if all_rxns[i] in GPR_rxns: + indices = [index for index, value in enumerate(GPR_rxns) if value == all_rxns[i]] + rxn_GPRS = indices + + # if rxns_GPRS not empty + if len(rxn_GPRS) != 0: + tmp_lst = [U_GPR_min[k] for k in rxn_GPRS] + E_X[i] = np.nanmax(tmp_lst) + + # for reactions with no corresponding probe in expression data + for i in range(len(is_C_H)): + if is_C_H[i] == 1: + E_X[i] = 1.0 + + return E_X diff --git a/pymcadre/rank/initialize_generic_model.py b/pymcadre/rank/initialize_generic_model.py new file mode 100644 index 0000000..50d23bf --- /dev/null +++ b/pymcadre/rank/initialize_generic_model.py @@ -0,0 +1,82 @@ +__author__ = "Nantia Leonidou" +__description__ = " Create a consistent generic model by removing all inactive reactions" + +# import numpy as np +# from cobra import * +# from rank.map_gene_scores_to_rxns import * +# from rank.parse_gprs import * +# from rank.calc_expr_evidence import * +# from cobra.flux_analysis import * +# from rank.map_high_conf_to_rxns import * +from prune.check_model_consistency import * +import math + + +def initialize_generic_model(model, C, E_X, confidence_scores, method=1): + """ This function creates a consistent generic model by removing all inactive + reactions. It will also return adjusted vectors for expression-based and + literature-based evidence, corresponding to the subset of reactions in + generic model GM. + + Input: + - model --> cobra.io.core.model.Model + - C --> list of Cobra core reactions + - E_X --> list of respective expression-based evidence + - confidence_scores --> experimental-based scores + - method --> fastFVA (1) or FASTCC (0) + + Output: + - GM --> generic model, includes only core reactions + - C --> list of Cobra core reactions + - E_X --> list of expression-based evidence + - E_L --> list of confidence level-based evidence""" + # define literature-based evidence from confidence_scores + if len(confidence_scores): + E_L = confidence_scores + + # reactions with no confidence information should not be ranked higher than + # those with non-zero confidence + for idx, elem in enumerate(E_L): + if math.isnan(elem): + E_L[idx] = 0 + else: + # create an empty list with zeros + E_L = [0.0] * len(model.reactions) + + # get inactive reactions + inactive_rxns = check_model_consistency(model, method)[0] + + # update core set of reactions + C = list(set(C) - set(inactive_rxns)) + + # create generic model by removing inactive reactions + GM = model.copy() + GM.remove_reactions(inactive_rxns, remove_orphans=True) + + # update list of expression-based evidence + GM_rxns_ids = [rxn.id for rxn in GM.reactions] # get reaction IDs from GM model + model_rxn_ids = [rxn.id for rxn in model.reactions] # get reaction IDs from initial model + + GM_idx = [] + model_idx = [] + for idx, i in enumerate(GM_rxns_ids): + for g_idx, j in enumerate(model_rxn_ids): + if i == j and g_idx not in model_idx: + model_idx.append(g_idx) + GM_idx.append(idx) + + E_X_GM = [0] * len(GM.reactions) + for i in range(len(GM_idx)): + E_X_GM[i] = E_X[model_idx[i]] + E_X = E_X_GM + + # update list of confidence level-based evidence + E_L_GM = [0] * len(GM.reactions) + for j in range(len(GM_idx)): + E_L_GM[j] = E_L[model_idx[j]] + E_L = E_L_GM + + return GM, C, E_X, E_L + + + diff --git a/pymcadre/rank/map_gene_scores_to_rxns.py b/pymcadre/rank/map_gene_scores_to_rxns.py new file mode 100644 index 0000000..db24281 --- /dev/null +++ b/pymcadre/rank/map_gene_scores_to_rxns.py @@ -0,0 +1,58 @@ +__author__ = "Nantia Leonidou" +__description__ = " Map gene ubiquity scores to reactions. " + +# from cobra import * +# from rank.parse_gprs import * +# from test_Inputs.test_Inputs import * +import numpy as np + + +def map_gene_scores_to_rxns(model, G, U, GPR_file): + """ Map gene ubiqiuty scores (i.e., how often a gene is expressed in tissue samples) to reactions + + Input: + - model --> cobra.io.core.model.Model + - G --> column vector, where each entry is the human- or mouse-specific Entrez ID for gene + - U --> numeric column vector, where each entry represents the calculated "ubiquity score" for the corresponding gene + - GPR_file + + Output: U_GPR --> list of lists, with ubiquity scores as float numbers""" + + # get all Entrez IDs from given model + genes = [] + for g in model.genes: + g = g.id + g = g.split('_')[0] + g = g.strip() + genes.append(g) + genes = [int(g) for g in genes] + + l = [len(GPR_file[i]) for i in range(len(GPR_file))] + # get the maximum and use it as number of columns, that C_H_GPR should maximally have + columns = max(l) + # create list of lists + U_GPR = [[np.nan for x in range(columns)] for y in range(len(GPR_file))] + + # get intersection of genes and G and their indices in G + gene_inter = list(set(G) & (set(genes))) + # which genes are in the intersection, sorted + gene_id = sorted([str(g) for g in gene_inter]) + # indexes of those genes in G + G_idx = [G.index(int(x)) for x in gene_id] + + + for gpr_idx in range(len(GPR_file)): + for gpr_idx_nested in range(len(GPR_file[gpr_idx])): + if GPR_file[gpr_idx][gpr_idx_nested] in gene_id: + get_idx = gene_id.index(GPR_file[gpr_idx][gpr_idx_nested]) + U_GPR[gpr_idx][gpr_idx_nested] = U[G_idx[get_idx]] + # now penalize genes with zero expression, such that corresponding reactions + # will be ranked lower than non-gene associated reactions. + for x in range(len(U_GPR)): + for y in range(len(U_GPR[x])): + if U_GPR[x][y] == float(0): + U_GPR[x][y] = -1e-6 + + return U_GPR + + diff --git a/pymcadre/rank/map_high_conf_to_rxns.py b/pymcadre/rank/map_high_conf_to_rxns.py new file mode 100644 index 0000000..5137540 --- /dev/null +++ b/pymcadre/rank/map_high_conf_to_rxns.py @@ -0,0 +1,68 @@ +__author__ = "Nantia Leonidou" +__description__ = " Map high confidence genes to reactions. " + +import numpy as np +# from rank.parse_gprs import * +# from test_Inputs.test_Inputs import * + + +def map_high_conf_to_rxns(model, GPR_file, GPR_rxns, C_H_genes=[]): + """ Map high confidence genes to reactions. + + Input: + - model --> cobra.io.core.model.Model + - GPR_file --> list of lists, containing gene IDs as strings + - GPR_rxns --> list of reaction IDs, obtained from GPRs, as strings + - C_H_genes --> list filled with Entrez IDs (as strings) for any genes with particularly strong evidence for activity in the selected tissue + Within the rank_reactions module, the reactions corresponding to these genes will automatically become + assigned to the "core" set to avoid removal. + + Output: + - is_C_H --> list of 0 or 1 indicating high confidence or not """ + + if len(C_H_genes) != 0: + # get all lengths of all sub-lists inside the GPR_file: + l = [len(GPR_file[i]) for i in range(len(GPR_file))] + # get the maximum and use it as number of columns, that C_H_GPR should maximally have + columns = max(l) + # check whether the input gene IDs from the C_H_genes file can be found in the GPR_file: + # create a list of same length as GPR_file, containing 1 if the + # ID from GPR_file can be found in C_H_genes list, 0 when it is not + # found and NaN otherwise + GPR_file = [[s.split('_')[0] for s in lst] for lst in GPR_file] # remove numbers after comma to match format of Entrez IDs + # # --> split('_') for R3con3D, split('.') for humanModel + new_GPR_file = [[r.strip() for r in lst] for lst in GPR_file] # remove unnecessary space before and after strings + + C_H_GPR = [[np.nan for x in range(columns)] for y in range(len(new_GPR_file))] + for i in range(len(new_GPR_file)): + for j in range(len(new_GPR_file[i])): + if new_GPR_file[i][j] in C_H_genes: + C_H_GPR[i][j] = 1 + else: + C_H_GPR[i][j] = 0 + + # get minimum value of each row (0 or 1) + C_H_GPR_min = [min(lst) for lst in C_H_GPR] + + # Is confidence high? + is_C_H = [0] * len(model.reactions) + + for idx,rxn in enumerate(model.reactions): + # compare current reaction ID to each row of the GPR_rxns, looking for an exact match of the entire character vector + rxn_GPRs = [] + for k in range(len(GPR_rxns)): + if rxn.id == GPR_rxns[k]: + rxn_GPRs.append(k) # if a match is found, store related indices from GPR_rxns file + if len(rxn_GPRs) != 0: + # based on reactions' indices, get corresponding values from the C_H_GPR_min + to_find_max = [C_H_GPR_min[index] for index in rxn_GPRs] + # store whether it is of high confidence + is_C_H[idx] = max(to_find_max) + # is_C_H = logical(is_C_H); + + else: + # if C_H_genes file is not provided, fill the list with zeros + is_C_H = [0] * len(model.reactions) + + return is_C_H + diff --git a/pymcadre/rank/parse_gprs.py b/pymcadre/rank/parse_gprs.py new file mode 100644 index 0000000..09700fb --- /dev/null +++ b/pymcadre/rank/parse_gprs.py @@ -0,0 +1,70 @@ +__author__ = "Nantia Leonidou" +__description__ = " Parse Gene–protein–reaction relationships (GPRs). " + +import re +# from cobra import * + + +def parse_gprs(model): + """ Parse Gene–protein–reaction relationships (GPRs) + + Input: model: cobra.io.core.model.Model + + Output: GPR_file with all gene IDs and GPR_rxns with all related reactions + + """ + + # get all gene-protein-reaction rules in the given model + # a string representation of the GPR rules defined in a readable format + # For example: - 9962.2 is the gene with the Entrez ID: 9962, that encodes 2 transcripts + # - 8706.3 is the gene with the Entrez ID: 8706, that encodes 3 transcripts + all_GPRS = [react.gene_reaction_rule for react in model.reactions] + # get number of totally involved genes in each rule + # possible cases: + # (1) 'or' and optionally 'and' --> occurrence of 'or' + 1 (cause above the first gene was not considered while counting the number of 'or' words) + # (2) only 'and' --> put 1 + # (3) nor 'or' or 'and' --> put 1 + # (4) empty cell --> put 0 + num_GPRS = [] + for gprs in all_GPRS: + if 'and' not in gprs and 'or' in gprs or 'and' in gprs and 'or' in gprs: + num_GPRS.append(gprs.count("or") + 1) + elif 'and' in gprs and 'or' not in gprs: + num_GPRS.append(1) + elif 'and' not in gprs and 'or' not in gprs and gprs != '': + num_GPRS.append(1) + else: + num_GPRS.append(0) + + num_rows = sum(num_GPRS) # number of total gene identifiers extracted from GPRs + num_cols = max(num_GPRS) + + # create an empty array with dimension: 5962x653 + GPR_file = [[0 for x in range(num_cols)] for y in range(num_rows)] + # create an empty array with dimensions 5962x1 + GPR_rxns = [[0 for x in range(1)] for y in range(num_rows)] + + count = 0 + for i in range(len(all_GPRS)): + if all_GPRS[i] != '': + # remove all 'or' words and keep only gene identifies + rule_GPRS = all_GPRS[i].split('or') + # remove parenthesis from gene identifies + rule_GPRS = [re.sub(r'[()]', '', rule) for rule in rule_GPRS] + for j in range(len(rule_GPRS)): + # remove 'and', when present in the rule + GPR = rule_GPRS[j].split('and') + # fill the GPR file with the gene IDs based on the GPR rules + # If a rule involves 'AND', the gene IDs will be written in the same row but different column + GPR_file[count] = GPR + # GPR_file[count][0:len(GPR)] = GPR + # fill the GPR_rxns file with the corresponding reaction + GPR_rxns[count] = model.reactions[i].id + count += 1 + + # remove comma-numbers to match format of Entrez IDs and unnecessary space before and after strings + GPR_file = [[y.split('_')[0] for y in x] for x in GPR_file] # --> split('_') for R3con3D, split('.') for humanModel + GPR_file = [[y.strip() for y in x] for x in GPR_file] + + return GPR_rxns, GPR_file + diff --git a/pymcadre/rank/rank_reactions.py b/pymcadre/rank/rank_reactions.py new file mode 100644 index 0000000..074bf26 --- /dev/null +++ b/pymcadre/rank/rank_reactions.py @@ -0,0 +1,121 @@ +__author__ = "Nantia Leonidou" +__description__ = " Rank reactions " + +from rank.parse_gprs import * +from rank.map_high_conf_to_rxns import * +from rank.map_gene_scores_to_rxns import * +from rank.calc_expr_evidence import * +from rank.initialize_generic_model import * +from rank.calc_conn_evidence import * +import math +import pandas as pd + + +def rank_reactions(model, G, U, confidence_scores, C_H_genes, method=1): + """ + Input: + - model (cobra.core.model.Model) + - G: gene IDs from expression data (lst) + - U: gene ubiquity scores (i.e., from mas5callToExpression) (lst) + - C_H_genes: high confidence genes (lst, optional) + - method: FVA(1, default) or FASTCC (2) (int) + + Output: + - GM: generic model with inactive reactions removed (cobra.core.model.Model) + - C: core reactions (lst) + - NC: non-core reactions (lst) + - P: removal order of non-core reactions (lst) """ + + ############################################### + # Parse GPRs + ############################################### + GPRrxns, GPRmat = parse_gprs(model) + + ############################################### + # Map high confidence genes to reactions + ############################################### + + if len(C_H_genes) != 0: + is_C_H = map_high_conf_to_rxns(model, GPRmat, GPRrxns, C_H_genes) + else: + is_C_H = [0] * len(model.reactions) + + ############################################### + # Map gene ubiqiuty scores to reactions + ############################################### + U_GPR = map_gene_scores_to_rxns(model, G, U, GPRmat) + + ############################################### + # Determine confidence level-based evidence + ############################################### + E_L = confidence_scores + + # Reactions with no confidence information should not be ranked higher than + # those with non-zero confidence + for idx, elem in enumerate(E_L): + if math.isnan(elem): + E_L[idx] = 0 + + ############################################### + # Calculate expression-based evidence + ############################################### + E_X = calc_expr_evidence(model, GPRrxns, U_GPR, is_C_H) + C = [] + for i in range(len(E_X)): + if E_X[i] > 0.9: + C.append(model.reactions[i].id) + model_C = C + + ###################################################################### + # Initialize the consistent generic model & update evidence vectors + ###################################################################### + GM, C, E_X, E_L = initialize_generic_model(model, C, E_X, confidence_scores, method) + R_G = GM.reactions + # get IDs + R_G_ids = [item.id for item in R_G] + + NC = [] + NC_idx = [] + for rg_idx, i in enumerate(R_G_ids): + if i not in C and i not in NC: + NC_idx.append(R_G.index(i)) + NC.append(i) + + ################################################ + # Calculate connectivity-based evidence + ################################################ + E_C = calc_conn_evidence(GM, E_X) # very slow due to matrix multiplication (2766x3742)*(3742x2766) + + ############################################### + # Rank non-core reactions + ############################################### + E_X_NC = [E_X[i] for i in NC_idx] # expression-based evidence for non-core reactions + E_C_NC = [E_C[i] for i in NC_idx] # connectivity-based evidence for non-core reactions + E_L_NC = [E_L[i] for i in NC_idx] # literature - based evidence for non - core reactions + # put all evidences in a singe list + data_tuples = list(zip(E_X_NC, E_C_NC, E_L_NC)) + # create data frame + df_evidence = pd.DataFrame(data_tuples, columns=['E_X_NC', 'E_C_NC', 'E_L_NC']) + # sort it + E_NC = df_evidence.sort_values(by=['E_X_NC', 'E_C_NC', 'E_L_NC']) + # get indices as a list + NC_order = list(E_NC.index) + + # ordered (ranked) non-core reactions + P = [NC[i] for i in NC_order] + + # convert data frame to numpy array, for easier analysis + E_NC = E_NC.T.to_numpy() + + ############################################### + # Identify zero-expression reactions + ############################################### + Z = [] + for i in range(len(E_NC[0])): + # print(i) + if E_NC[0][i] == -1e-6: + # print(E_NC['E_X_NC'][i]) + Z.append(P[i]) + + print('rank_reactions done ... ') + return GM, C, NC, P, Z, model_C diff --git a/pymcadre/test_scripts/python_recon1_with_BOF_and_VBOF__BEC1_method2.ipynb b/pymcadre/test_scripts/python_recon1_with_BOF_and_VBOF__BEC1_method2.ipynb new file mode 100644 index 0000000..012c0b3 --- /dev/null +++ b/pymcadre/test_scripts/python_recon1_with_BOF_and_VBOF__BEC1_method2.ipynb @@ -0,0 +1,16222 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "__author__ = \"Nantia Leonidou\"\n", + "__description__ = \" Main script \"\n", + "########################################\n", + "# copied from run_mcadre.py\n", + "########################################\n", + "\n", + "from test_Inputs.test_Inputs import *\n", + "import pandas as pd\n", + "import numpy as np\n", + "\n", + "# read model\n", + "model = io.read_sbml_model('../../test_dataset/recon1_with_BOF_and_VBOF.xml')\n", + "# genes\n", + "G = pd.read_csv('../../test_dataset/1_GPL570_GSE3397/1_GPL570_GSE3397_entrez_ids.csv'')\n", + "G = list(G['ENTREZ_GENE_ID'])\n", + "# ubiquity scores\n", + "U = pd.read_csv('../../test_dataset/1_GPL570_GSE3397/1_GPL570_GSE3397_ubiquity.csv', header=None)\n", + "U = U.rename(columns={0: \"Scores\"})\n", + "U = list(U['Scores'])\n", + "#confidence_scores\n", + "confidence_scores = pd.read_csv('../../test_dataset/Recon1_confidence_scores_with_BOF_and_VBOF.csv')\n", + "confidence_scores = np.float64(list(confidence_scores['Confidence Score']))" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/Users/leonidou/Documents/mCADRE_PYTHON_code/code/rank/calc_expr_evidence.py:34 \u001b[1;31mRuntimeWarning\u001b[0m: All-NaN axis encountered\n", + "/Users/leonidou/Documents/mCADRE_PYTHON_code/code/rank/calc_expr_evidence.py:58 \u001b[1;31mRuntimeWarning\u001b[0m: All-NaN axis encountered\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Checking all reactions (FASTCC)...\n", + "Model consists of 1317 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 14.221331999999997\n", + "check_model_consistency done ... \n", + "rank_reactions done ... \n" + ] + } + ], + "source": [ + "from rank.rank_reactions import *\n", + "GM, C, NC, P, Z, model_C = rank_reactions(model, G, U, confidence_scores, [], 2)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "2426" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(GM.reactions)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "1583" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(GM.metabolites)" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "1475" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(GM.genes)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "851" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(C)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "1575" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(NC)" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "1322" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(model_C)" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Generic model passed precursor metabolites test\n", + "Pruning reactions...\n", + "Reaction no. 1\n", + "Attempting to remove reaction: THMMPt4 ...\n", + "Initial PM reactions: 2426\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 21 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.4890180000000157\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 22 , inactive_C: ['FACOAL240', 'FACOAL200', 'GALT'], inactive_NC:['EX_gal_e', 'CYTK9n', 'EX_ha_e', 'PAIL4P_HStn', 'EX_udp_e', 'EX_lgnc_e', 'CHOLATEt', 'RAI4', 'EX_arach_e', 'EX_chsterol_e', 'EX_thmmp_e', 'EX_10fthf5glu_e', 'TCHOLAte', 'EX_fru_e', 'ASCBt', 'ESTRADIOLGLCt', 'EX_ump_e', 'THMMPt4', 'OCDCEAt']\n", + "Zero-expression evidence for reaction...\n", + "2426\n", + "2426\n", + "check_model_function done ....\n", + "PM reactions (before): 2426\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2404\n", + "Num. removed: 22 (3 core, 19 non-core); Num. remaining: 1556\n", + "Reaction no. 2\n", + "Attempting to remove reaction: DCT ...\n", + "Initial PM reactions: 2404\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.7508359999999925\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['HSD17B1', 'PSSA1_hs', 'FATP3t', 'COAtim'], inactive_NC:['RIBt', 'DCT', 'DOPACHRMISO', 'DM_melanin_c', 'CYTK11n', 'ARTPLM3', 'TYRASE', 'DOPAQNISO1', 'PAIL45P_HStn', 'TYRDOPO3', 'ESTRADIOLtr']\n", + "Zero-expression evidence for reaction...\n", + "2404\n", + "2404\n", + "check_model_function done ....\n", + "Len P: 1556\n", + "num_removed 22\n", + "Len P AFTER 1555\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 22 (3 core, 19 non-core); Num. remaining: 1555\n", + "Reaction no. 3\n", + "Attempting to remove reaction: TYRASE ...\n", + "Initial PM reactions: 2404\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 23 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.652152000000001\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 24 , inactive_C: ['HSD17B1', 'MANt1r'], inactive_NC:['DCT', 'RIBt', 'DOPACHRMISO', 'OCDCAt', 'DM_melanin_c', 'EX_ascb__L_e', 'EX_adprib_e', 'HDCAt', '5MTHFt2', 'ACt2m', 'ESTRADIOLtr', 'TYRDOPO3', 'EX_glyb_e', 'GLYBt4_2_r', 'GULNDer', 'TRPt', 'EX_so4_e', 'EX_dhdascb_e', 'EX_hdca_e', 'TYRASE', 'DOPAQNISO1', 'EX_gluala_e']\n", + "Zero-expression evidence for reaction...\n", + "2404\n", + "2404\n", + "check_model_function done ....\n", + "PM reactions (before): 2404\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2380\n", + "Num. removed: 46 (5 core, 41 non-core); Num. remaining: 1534\n", + "Reaction no. 4\n", + "Attempting to remove reaction: ACOX22x ...\n", + "Initial PM reactions: 2380\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 17 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.440226999999993\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 18 , inactive_C: ['SCP2x', 'FACOAL204_copy1'], inactive_NC:['EX_pi_e', 'ACOX22x', 'AMACR2p', 'DGCHOLtx', 'GLYCt', 'FATP5t', 'HSD17B42x', 'FATP7t', 'TCHOLAt', 'EX_hdcea_e', 'DTTPtn', 'DGCHOLte', 'EX_dgchol_e', 'ORNt4m', 'BAAT3x', 'HDCEAt']\n", + "Zero-expression evidence for reaction...\n", + "2380\n", + "2380\n", + "check_model_function done ....\n", + "Len P: 1534\n", + "num_removed 46\n", + "Len P AFTER 1533\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 46 (5 core, 41 non-core); Num. remaining: 1533\n", + "Reaction no. 5\n", + "Attempting to remove reaction: AMACRp ...\n", + "Initial PM reactions: 2380\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 34 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.697240999999991\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 35 , inactive_C: ['SCPx', 'THYOXt2', 'FACOAL204_copy1', 'PSSA1_hs', 'NDPK1m'], inactive_NC:['P45027A12m', 'CYTK14', 'EX_tchola_e', 'XOLTRIOLtm', 'MALTSULtm', 'GLYtp', 'BAAT2x', 'P45027A13m', 'P4508B11r', 'P45027A11m', 'TCHOLAt', 'ARACHDt2', 'TCHOLAtx', 'GCHOLAt', 'AKR1C42', 'VLCSp', 'THCHOLSTOICtm', 'GCHOLAtx', 'HSD17B4x', 'AMACRp', 'ACOX2x', 'EX_gchola_e', 'XOLDIOLONEt', 'MALSO3tm', 'AKR1D2', 'CPK1', 'EX_gsn_e', 'P4508B13r', 'BAAT1x', 'ORNt4m']\n", + "Zero-expression evidence for reaction...\n", + "2380\n", + "2380\n", + "check_model_function done ....\n", + "PM reactions (before): 2380\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2345\n", + "Num. removed: 81 (10 core, 71 non-core); Num. remaining: 1503\n", + "Reaction no. 6\n", + "Attempting to remove reaction: 34DHPHEt ...\n", + "Initial PM reactions: 2345\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 24 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.557379999999995\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 25 , inactive_C: ['DCK1n', 'RAI3', 'DAGK_hs', 'ILEtec', 'NDPK3', 'MAN6PI', 'PGMT'], inactive_NC:['CYTK8', 'SPHS1Pte', 'EX_9_cis_retfa_e', 'H2O2tm', 'DINt', '34DHPHEt', 'EX_34dhphe_e', 'TAURt4_2_r', 'CHLtm', 'DRIBt', 'TYRt', 'EX_sphs1p_e', 'SUCCt4_2', 'DTTPtn', 'SRTNt6_2_r', 'EX_taur_e', 'PAIL45P_HStn', 'EX_drib_e']\n", + "Zero-expression evidence for reaction...\n", + "2345\n", + "2345\n", + "check_model_function done ....\n", + "Len P: 1503\n", + "num_removed 81\n", + "Len P AFTER 1502\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 81 (10 core, 71 non-core); Num. remaining: 1502\n", + "Reaction no. 7\n", + "Attempting to remove reaction: SRTNtu ...\n", + "Initial PM reactions: 2345\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.640784999999994\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: [], inactive_NC:['SRTNtu', 'EX_9_cis_retfa_e', 'O2Stm', 'EX_glu__L_e']\n", + "Zero-expression evidence for reaction...\n", + "2345\n", + "2345\n", + "check_model_function done ....\n", + "PM reactions (before): 2345\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2341\n", + "Num. removed: 85 (10 core, 75 non-core); Num. remaining: 1498\n", + "Reaction no. 8\n", + "Attempting to remove reaction: DEBRISOQUINEt ...\n", + "Initial PM reactions: 2341\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.4279870000000017\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: [], inactive_NC:['P4502D6', 'DEBRISOQUINEt', 'CHLtm', 'EX_hdcea_e', 'DTTPtn', 'EX_debrisoquine_e', 'EX_4hdebrisoquine_e', '4HDEBRISOQUINEte', 'RAI1', 'HDCEAt']\n", + "Zero-expression evidence for reaction...\n", + "2341\n", + "2341\n", + "check_model_function done ....\n", + "PM reactions (before): 2341\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2331\n", + "Num. removed: 95 (10 core, 85 non-core); Num. remaining: 1488\n", + "Reaction no. 9\n", + "Attempting to remove reaction: CHATn ...\n", + "Initial PM reactions: 2331\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 12 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.4982880000000023\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 13 , inactive_C: ['ACETONEt2'], inactive_NC:['CHOLtn', 'EX_acetone_e', 'ACHtn', 'MANt4', 'COAtn', 'EX_man_e', 'CHATn', 'PE_HStm', 'H2O2tm', 'PAIL45P_HStn', 'EX_amp_e', 'ACCOAtn']\n", + "Zero-expression evidence for reaction...\n", + "2331\n", + "2331\n", + "check_model_function done ....\n", + "PM reactions (before): 2331\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2318\n", + "Num. removed: 108 (11 core, 97 non-core); Num. remaining: 1476\n", + "Reaction no. 10\n", + "Attempting to remove reaction: CSNt ...\n", + "Initial PM reactions: 2318\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.096858999999995\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['NDPK5'], inactive_NC:['CSNt', 'EX_retinol_e', 'CSND', 'EX_crvnc_e', 'EX_csn_e', 'ABTD', 'BILGLCURt']\n", + "Zero-expression evidence for reaction...\n", + "2318\n", + "2318\n", + "check_model_function done ....\n", + "PM reactions (before): 2318\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2310\n", + "Num. removed: 116 (12 core, 104 non-core); Num. remaining: 1469\n", + "Reaction no. 11\n", + "Attempting to remove reaction: 5FTHFt2 ...\n", + "Initial PM reactions: 2310\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.3744199999999864\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['FUMm'], inactive_NC:['34DHPHEt', 'ADKd', 'EX_5fthf_e', 'EX_34dhphe_e', 'EX_inost_e', 'FTHFCL', 'HSD3A2r', '5FTHFt2', 'GLYCt']\n", + "Zero-expression evidence for reaction...\n", + "2310\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2310\n", + "check_model_function done ....\n", + "PM reactions (before): 2310\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2300\n", + "Num. removed: 126 (13 core, 113 non-core); Num. remaining: 1461\n", + "Reaction no. 12\n", + "Attempting to remove reaction: ADPRIBt ...\n", + "Initial PM reactions: 2300\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 16 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.3683320000000094\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 17 , inactive_C: ['DCK1n', 'DCMPDA', 'DAGK_hs', 'ACACT1r_copy2', 'GALt1r', 'THD1m', 'RPI', 'COAtim'], inactive_NC:['EX_din_e', 'CYTK9', 'NADNe', 'ADPRIBt', 'SPH1Pte', 'EX_nad_e', 'EX_sph1p_e', 'EX_ncam_e', 'CLPNDCOAtx']\n", + "Zero-expression evidence for reaction...\n", + "2300\n", + "2300\n", + "check_model_function done ....\n", + "Len P: 1461\n", + "num_removed 126\n", + "Len P AFTER 1460\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 126 (13 core, 113 non-core); Num. remaining: 1460\n", + "Reaction no. 13\n", + "Attempting to remove reaction: PGDI ...\n", + "Initial PM reactions: 2300\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.6256779999999935\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['DCK2n', 'PGS'], inactive_NC:['EX_prostgd2_e', 'PROSTGD2t', 'PGDI']\n", + "Zero-expression evidence for reaction...\n", + "2300\n", + "2300\n", + "check_model_function done ....\n", + "Len P: 1460\n", + "num_removed 126\n", + "Len P AFTER 1459\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 126 (13 core, 113 non-core); Num. remaining: 1459\n", + "Reaction no. 14\n", + "Attempting to remove reaction: THMTPt ...\n", + "Initial PM reactions: 2300\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.0754799999999705\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['ORNTArm', 'DAGK_hs', '5MTHFt', 'THMt3', 'FOLR2', 'LEUtec'], inactive_NC:['EX_thm_e', 'FOLt2', 'EX_thmtp_e', 'CLOHtex2', 'EX_5mthf_e', 'EX_fol_e', 'NMNAT', 'ORNt3m', 'THMTPt']\n", + "Zero-expression evidence for reaction...\n", + "2300\n", + "2300\n", + "check_model_function done ....\n", + "Len P: 1459\n", + "num_removed 126\n", + "Len P AFTER 1458\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 126 (13 core, 113 non-core); Num. remaining: 1458\n", + "Reaction no. 15\n", + "Attempting to remove reaction: AGTix ...\n", + "Initial PM reactions: 2300\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 31 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.6157210000000077\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 32 , inactive_C: ['ILEtec', 'SCP2x', 'HPYRRy', 'LALDO', 'HPYRR2x'], inactive_NC:['BAAT4x', 'EX_glyc__S_e', 'EX_taur_e', 'HSD17B42x', 'TAURt4_2_r', 'FADH2tx', 'EX_gdchola_e', 'DGCHOLte', 'EX_dgchol_e', 'BAAT3x', 'SERtp', 'GLYOp', 'ACOX22x', 'AMACR2p', 'AGTix', 'DGCHOLtx', 'HPYRDC', 'GDCHOLAtx', 'H2O2tp', 'EX_xylt_e', 'FADtx', 'HPYRtp', 'GDCHOLAte', 'GLYC_St', 'XYLTt', 'SPTix', 'GLYCK2']\n", + "Zero-expression evidence for reaction...\n", + "2300\n", + "2300\n", + "check_model_function done ....\n", + "PM reactions (before): 2300\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2268\n", + "Num. removed: 158 (18 core, 140 non-core); Num. remaining: 1432\n", + "Reaction no. 16\n", + "Attempting to remove reaction: PROSTGF2t ...\n", + "Initial PM reactions: 2268\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.0741989999999646\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CBR2'], inactive_NC:['PROSTGF2t', 'RDH2', 'ALAGLYexR', 'EX_prostgf2_e', 'EX_prostge2_e']\n", + "Zero-expression evidence for reaction...\n", + "2268\n", + "2268\n", + "check_model_function done ....\n", + "PM reactions (before): 2268\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2262\n", + "Num. removed: 164 (19 core, 145 non-core); Num. remaining: 1427\n", + "Reaction no. 17\n", + "Attempting to remove reaction: ACGAM2E ...\n", + "Initial PM reactions: 2262\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 15 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.4794619999999554\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 16 , inactive_C: ['ORNTArm', 'SIAASEly', 'GALASE1ly', 'GASNASEly', 'TPI', 'UAG2EMA', 'AHEXASEly', 'ACNAMlt', 'FUCASEe'], inactive_NC:['ENGASEly', 'ACGAM2E', 'EX_s2l2fn2m2masn_e', 'UMPK5', 'S2L2N2M2MASNtly', 'CYTK1', 'GALtly']\n", + "Zero-expression evidence for reaction...\n", + "2262\n", + "2262\n", + "check_model_function done ....\n", + "Len P: 1427\n", + "num_removed 164\n", + "Len P AFTER 1426\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 164 (19 core, 145 non-core); Num. remaining: 1426\n", + "Reaction no. 18\n", + "Attempting to remove reaction: THYMt ...\n", + "Initial PM reactions: 2262\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.336488999999972\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['DCK2n', 'PUNP6', 'PGMT', 'DAGK_hs'], inactive_NC:['THYMt', 'EX_thym_e']\n", + "Zero-expression evidence for reaction...\n", + "2262\n", + "2262\n", + "check_model_function done ....\n", + "Len P: 1426\n", + "num_removed 164\n", + "Len P AFTER 1425\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 164 (19 core, 145 non-core); Num. remaining: 1425\n", + "Reaction no. 19\n", + "Attempting to remove reaction: HIStiDF ...\n", + "Initial PM reactions: 2262\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.0129440000000045\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['DCK2n', 'ORNTArm', 'DAGK_hs'], inactive_NC:['EX_cit_e', 'PROtm', 'ORNt3m', 'HMGCOAtm', 'HIStiDF']\n", + "Zero-expression evidence for reaction...\n", + "2262\n", + "2262\n", + "check_model_function done ....\n", + "Len P: 1425\n", + "num_removed 164\n", + "Len P AFTER 1424\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 164 (19 core, 145 non-core); Num. remaining: 1424\n", + "Reaction no. 20\n", + "Attempting to remove reaction: LCAT1e ...\n", + "Initial PM reactions: 2262\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.349156999999991\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['ACONTm'], inactive_NC:['ARTPLM3', 'SPH1Pte', 'EX_sph1p_e', 'EX_xolest2_hs_e', 'CHSTEROLt', 'CLPNDCOAtx', 'LCAT1e']\n", + "Zero-expression evidence for reaction...\n", + "2262\n", + "2262\n", + "check_model_function done ....\n", + "PM reactions (before): 2262\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2254\n", + "Num. removed: 172 (20 core, 152 non-core); Num. remaining: 1417\n", + "Reaction no. 21\n", + "Attempting to remove reaction: NNMT ...\n", + "Initial PM reactions: 2254\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 21 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.0506829999999923\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 22 , inactive_C: ['FACOAL1831', 'NP1', 'FACOAL2252'], inactive_NC:['FRUt1r', 'LDH_D', 'EX_clpnd_e', 'NACt', 'SERGLNexR', 'LNLNCGt', 'EX_nac_e', 'QUILSYN', 'UMPK6', 'CLPNDt', 'EX_1mncam_e', 'NNMT', 'NNDPR', '1MNCAMti', 'NADS2', 'NCAMUP', 'PROtm', 'INSTt2', 'EX_lnlncg_e']\n", + "Zero-expression evidence for reaction...\n", + "2254\n", + "2254\n", + "check_model_function done ....\n", + "PM reactions (before): 2254\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2232\n", + "Num. removed: 194 (23 core, 171 non-core); Num. remaining: 1398\n", + "Reaction no. 22\n", + "Attempting to remove reaction: FOLt2 ...\n", + "Initial PM reactions: 2232\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.383489999999995\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['5MTHFt', 'CRNt_copy1', 'FOLR2', 'TMDPP'], inactive_NC:['EX_5mthf_e', 'FOLt2', 'EX_fol_e']\n", + "Zero-expression evidence for reaction...\n", + "2232\n", + "2232\n", + "check_model_function done ....\n", + "Len P: 1398\n", + "num_removed 194\n", + "Len P AFTER 1397\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 194 (23 core, 171 non-core); Num. remaining: 1397\n", + "Reaction no. 23\n", + "Attempting to remove reaction: URAt ...\n", + "Initial PM reactions: 2232\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 13 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.3320229999999924\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 14 , inactive_C: ['DCMPDA', 'DAGK_hs', 'CRNt_copy1', 'PGMT', 'FACOAL205', 'NDPK7m'], inactive_NC:['CYTK8', 'SPHS1Pte', 'TMNDNCt', 'EX_tmndnc_e', 'EX_sphs1p_e', 'UREAt5', 'EX_ura_e', 'URAt']\n", + "Zero-expression evidence for reaction...\n", + "2232\n", + "2232\n", + "check_model_function done ....\n", + "Len P: 1397\n", + "num_removed 194\n", + "Len P AFTER 1396\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 194 (23 core, 171 non-core); Num. remaining: 1396\n", + "Reaction no. 24\n", + "Attempting to remove reaction: HYXNt ...\n", + "Initial PM reactions: 2232\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.018470000000036\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['DAGK_hs'], inactive_NC:['SUCCt4_2', 'HYXNt', 'EX_hxan_e']\n", + "Zero-expression evidence for reaction...\n", + "2232\n", + "2232\n", + "check_model_function done ....\n", + "PM reactions (before): 2232\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2228\n", + "Num. removed: 198 (24 core, 174 non-core); Num. remaining: 1393\n", + "Reaction no. 25\n", + "Attempting to remove reaction: GUAt ...\n", + "Initial PM reactions: 2228\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.2161009999999806\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['LALDD', 'ASPTAm'], inactive_NC:['GUAt', 'EX_gua_e']\n", + "Zero-expression evidence for reaction...\n", + "2228\n", + "2228\n", + "check_model_function done ....\n", + "Len P: 1393\n", + "num_removed 198\n", + "Len P AFTER 1392\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 198 (24 core, 174 non-core); Num. remaining: 1392\n", + "Reaction no. 26\n", + "Attempting to remove reaction: L_LACtcm ...\n", + "Initial PM reactions: 2228\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.164436999999964\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['ORNTArm', 'LALDD', 'FACOAL246_1', 'LDH_L', 'NDPK3', 'FACOAL205'], inactive_NC:['TMNDNCt', 'TETHEX3t', 'EX_tmndnc_e', 'L_LACtcm', 'UMPK5', 'TYRt', 'EX_tethex3_e', 'UREAt5', 'RDH1']\n", + "Zero-expression evidence for reaction...\n", + "2228\n", + "2228\n", + "check_model_function done ....\n", + "Len P: 1392\n", + "num_removed 198\n", + "Len P AFTER 1391\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 198 (24 core, 174 non-core); Num. remaining: 1391\n", + "Reaction no. 27\n", + "Attempting to remove reaction: AMETt2m ...\n", + "Initial PM reactions: 2228\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 25 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.0754380000000197\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 26 , inactive_C: ['FBA', 'PETOHMm_hs', 'CYTDtm', 'CDSm', 'NDPK3m'], inactive_NC:['PSDm_hs', 'SPHS1Pte', 'AMETt2m', 'GLYBtm', 'DMGtm', 'BETALDHxm', 'PCFLOPm', 'PCHOLPm_hs', 'BHMT', 'CDPDAGtm', 'CHOLD2m', 'PSFLIPm', 'CYTK1m', 'DMGDHm', 'FALDtm', 'PEFLIPm', 'ARTPLM2', 'RPE', 'CYTDK2m', 'EX_sphs1p_e', 'H2Otm']\n", + "Zero-expression evidence for reaction...\n", + "2228\n", + "2228\n", + "check_model_function done ....\n", + "PM reactions (before): 2228\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2202\n", + "Num. removed: 224 (29 core, 195 non-core); Num. remaining: 1370\n", + "Reaction no. 28\n", + "Attempting to remove reaction: TXASr ...\n", + "Initial PM reactions: 2202\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.266754999999989\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['PGSr'], inactive_NC:['TXA2tr', 'EX_txa2_e', 'UREAt5', 'TXA2te', 'TXASr', 'ARACHDtr']\n", + "Zero-expression evidence for reaction...\n", + "2202\n", + "2202\n", + "check_model_function done ....\n", + "PM reactions (before): 2202\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2195\n", + "Num. removed: 231 (30 core, 201 non-core); Num. remaining: 1364\n", + "Reaction no. 29\n", + "Attempting to remove reaction: PROSTGE2t2 ...\n", + "Initial PM reactions: 2195\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.25871699999999\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['DCK2n', 'DCMPDA'], inactive_NC:['CYTK7n', 'PROSTGE2t2']\n", + "Zero-expression evidence for reaction...\n", + "2195\n", + "2195\n", + "check_model_function done ....\n", + "Len P: 1364\n", + "num_removed 231\n", + "Len P AFTER 1363\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 231 (30 core, 201 non-core); Num. remaining: 1363\n", + "Reaction no. 30\n", + "Attempting to remove reaction: SERDGLYexR ...\n", + "Initial PM reactions: 2195\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9386769999999842\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['NDPK8m', 'HSD11B1r'], inactive_NC:['HSD11B2r', 'SERDGLNexR', 'Htr', 'DOPAtu', 'SERDGLYexR', 'H2Oter']\n", + "Zero-expression evidence for reaction...\n", + "2195\n", + "2195\n", + "check_model_function done ....\n", + "PM reactions (before): 2195\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2187\n", + "Num. removed: 239 (32 core, 207 non-core); Num. remaining: 1357\n", + "Reaction no. 31\n", + "Attempting to remove reaction: TYRt ...\n", + "Initial PM reactions: 2187\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.21134399999994\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['DCK1n', 'CRNt_copy1', 'PGMT'], inactive_NC:['RADH4', 'CYTK7n', 'TYRt', 'UMPK3']\n", + "Zero-expression evidence for reaction...\n", + "2187\n", + "2187\n", + "check_model_function done ....\n", + "Len P: 1357\n", + "num_removed 239\n", + "Len P AFTER 1356\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 239 (32 core, 207 non-core); Num. remaining: 1356\n", + "Reaction no. 32\n", + "Attempting to remove reaction: CYTK6n ...\n", + "Initial PM reactions: 2187\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.25768800000003\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['CRNt_copy1', 'PGMT'], inactive_NC:['CYTK3', 'CYTK6n']\n", + "Zero-expression evidence for reaction...\n", + "2187\n", + "2187\n", + "check_model_function done ....\n", + "Len P: 1356\n", + "num_removed 239\n", + "Len P AFTER 1355\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 239 (32 core, 207 non-core); Num. remaining: 1355\n", + "Reaction no. 33\n", + "Attempting to remove reaction: It ...\n", + "Initial PM reactions: 2187\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9783670000000484\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['DCK2n', 'ASPTA'], inactive_NC:['CYTK7n', 'It', 'RETI2']\n", + "Zero-expression evidence for reaction...\n", + "2187\n", + "2187\n", + "check_model_function done ....\n", + "Len P: 1355\n", + "num_removed 239\n", + "Len P AFTER 1354\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 239 (32 core, 207 non-core); Num. remaining: 1354\n", + "Reaction no. 34\n", + "Attempting to remove reaction: ADEt ...\n", + "Initial PM reactions: 2187\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.2095669999999927\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['THD1m', 'CRNt_copy1'], inactive_NC:['EX_ade_e', 'CYTK2_1', 'ADEt']\n", + "Zero-expression evidence for reaction...\n", + "2187\n", + "2187\n", + "check_model_function done ....\n", + "Len P: 1354\n", + "num_removed 239\n", + "Len P AFTER 1353\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 239 (32 core, 207 non-core); Num. remaining: 1353\n", + "Reaction no. 35\n", + "Attempting to remove reaction: CYTK3 ...\n", + "Initial PM reactions: 2187\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.3155779999999595\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['CYTK3', 'CYTK7n']\n", + "Zero-expression evidence for reaction...\n", + "2187\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2187\n", + "check_model_function done ....\n", + "PM reactions (before): 2187\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2185\n", + "Num. removed: 241 (32 core, 209 non-core); Num. remaining: 1351\n", + "Reaction no. 36\n", + "Attempting to remove reaction: CYTK8n ...\n", + "Initial PM reactions: 2185\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.921842999999967\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['DCK1n', 'NDPK8n', 'FACOAL246_1', 'CRNt_copy1', 'PGMT', 'FACOAL203'], inactive_NC:['TETHEX3t', 'DLNLCGt', 'EX_tethex3_e', 'EX_dlnlcg_e', 'CYTK8n']\n", + "Zero-expression evidence for reaction...\n", + "2185\n", + "2185\n", + "check_model_function done ....\n", + "Len P: 1351\n", + "num_removed 241\n", + "Len P AFTER 1350\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 241 (32 core, 209 non-core); Num. remaining: 1350\n", + "Reaction no. 37\n", + "Attempting to remove reaction: CYTK10n ...\n", + "Initial PM reactions: 2185\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.217520000000036\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['DCK1n', 'NDPK1n', 'FACOAL2251'], inactive_NC:['ADK3', 'EX_dcsptn1_e', 'CYTK2_1', 'CYTK10n', 'DCSPTN1t']\n", + "Zero-expression evidence for reaction...\n", + "2185\n", + "2185\n", + "check_model_function done ....\n", + "Len P: 1350\n", + "num_removed 241\n", + "Len P AFTER 1349\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 241 (32 core, 209 non-core); Num. remaining: 1349\n", + "Reaction no. 38\n", + "Attempting to remove reaction: CYTK5n ...\n", + "Initial PM reactions: 2185\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.1289689999999837\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['CRNt_copy1', 'PGMT'], inactive_NC:['EX_din_e', 'RADH3', 'EX_uri_e', 'TYRt', 'EX_ser__L_e', 'CYTK5n']\n", + "Zero-expression evidence for reaction...\n", + "2185\n", + "2185\n", + "check_model_function done ....\n", + "PM reactions (before): 2185\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2177\n", + "Num. removed: 249 (34 core, 215 non-core); Num. remaining: 1344\n", + "Reaction no. 39\n", + "Attempting to remove reaction: GCC2bim ...\n", + "Initial PM reactions: 2177\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9485770000000002\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['GCC2bim', 'GCC2cm', 'GCC2am', 'DRIBt', 'EX_drib_e']\n", + "Zero-expression evidence for reaction...\n", + "2177\n", + "2177\n", + "check_model_function done ....\n", + "PM reactions (before): 2177\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2172\n", + "Num. removed: 254 (34 core, 220 non-core); Num. remaining: 1339\n", + "Reaction no. 40\n", + "Attempting to remove reaction: GCCbim ...\n", + "Initial PM reactions: 2172\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.2983579999998938\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['FACOAL205'], inactive_NC:['GCCam', 'TMNDNCt', 'EX_tmndnc_e', 'GCCbim', 'EX_thym_e', 'THYMt', 'GCCcm']\n", + "Zero-expression evidence for reaction...\n", + "2172\n", + "2172\n", + "check_model_function done ....\n", + "PM reactions (before): 2172\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2164\n", + "Num. removed: 262 (35 core, 227 non-core); Num. remaining: 1333\n", + "Reaction no. 41\n", + "Attempting to remove reaction: ALADGLYexR ...\n", + "Initial PM reactions: 2164\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.359017999999992\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['NDPK1n'], inactive_NC:['ALADGLYexR']\n", + "Zero-expression evidence for reaction...\n", + "2164\n", + "2164\n", + "check_model_function done ....\n", + "Len P: 1333\n", + "num_removed 262\n", + "Len P AFTER 1332\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 262 (35 core, 227 non-core); Num. remaining: 1332\n", + "Reaction no. 42\n", + "Attempting to remove reaction: HISDr ...\n", + "Initial PM reactions: 2164\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.1953719999999066\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: [], inactive_NC:['GluForTx', 'IZPN', 'FTCD', 'RETI2', 'HISDr', 'URCN']\n", + "Zero-expression evidence for reaction...\n", + "2164\n", + "2164\n", + "check_model_function done ....\n", + "PM reactions (before): 2164\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2158\n", + "Num. removed: 268 (35 core, 233 non-core); Num. remaining: 1326\n", + "Reaction no. 43\n", + "Attempting to remove reaction: BCDO ...\n", + "Initial PM reactions: 2158\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.1696289999999863\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['NDPK4m', 'AACOAT', 'ACACT1r_copy2', 'MAN6PI', 'INSt'], inactive_NC:['CYTK10', 'EX_caro_e', 'BCDO', 'CAROtr']\n", + "Zero-expression evidence for reaction...\n", + "2158\n", + "2158\n", + "check_model_function done ....\n", + "Len P: 1326\n", + "num_removed 268\n", + "Len P AFTER 1325\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 268 (35 core, 233 non-core); Num. remaining: 1325\n", + "Reaction no. 44\n", + "Attempting to remove reaction: ALOX5 ...\n", + "Initial PM reactions: 2158\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 22 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.2592590000000428\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 23 , inactive_C: ['DCK2n', 'ORNTArm', 'PUNP5', 'LTC4Sr', 'NDPK3', 'CHOLtu', 'VALTAim'], inactive_NC:['H2CO3Dm', 'LEUKTRC4t', 'GTHRDtr', 'LEUKTRD4tr', 'LEUKTRA4tr', 'ALOX5', 'GLUtr', 'LTD4DP', 'GGT5r', 'H2CO3D2m', 'VALt5m', 'LTC4CP', 'EX_leuktrC4_e', 'ALOX52', 'PROSTGE2t2', 'GGT6']\n", + "Zero-expression evidence for reaction...\n", + "2158\n", + "2158\n", + "check_model_function done ....\n", + "Len P: 1325\n", + "num_removed 268\n", + "Len P AFTER 1324\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 268 (35 core, 233 non-core); Num. remaining: 1324\n", + "Reaction no. 45\n", + "Attempting to remove reaction: TRPO2 ...\n", + "Initial PM reactions: 2158\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.0606970000000047\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['ORNTArm', 'HKYNH'], inactive_NC:['TRPO2', 'AMCOXO', 'KYN3OX', 'UMPK4n', 'FKYNH', 'AM6SAD', 'PCLAD', '3HAO']\n", + "Zero-expression evidence for reaction...\n", + "2158\n", + "2158\n", + "check_model_function done ....\n", + "PM reactions (before): 2158\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2148\n", + "Num. removed: 278 (37 core, 241 non-core); Num. remaining: 1316\n", + "Reaction no. 46\n", + "Attempting to remove reaction: CYTK12n ...\n", + "Initial PM reactions: 2148\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.2164209999999684\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['DCK2n', 'PUNP4'], inactive_NC:['CYTK12n']\n", + "Zero-expression evidence for reaction...\n", + "2148\n", + "2148\n", + "check_model_function done ....\n", + "Len P: 1316\n", + "num_removed 278\n", + "Len P AFTER 1315\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 278 (37 core, 241 non-core); Num. remaining: 1315\n", + "Reaction no. 47\n", + "Attempting to remove reaction: UMPK6n ...\n", + "Initial PM reactions: 2148\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.1747649999999794\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['NDPK2n'], inactive_NC:['ORNt3m', 'UMPK6n']\n", + "Zero-expression evidence for reaction...\n", + "2148\n", + "2148\n", + "check_model_function done ....\n", + "Len P: 1315\n", + "num_removed 278\n", + "Len P AFTER 1314\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 278 (37 core, 241 non-core); Num. remaining: 1314\n", + "Reaction no. 48\n", + "Attempting to remove reaction: UMPK2n ...\n", + "Initial PM reactions: 2148\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8333390000000236\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['DCK2n', 'ADNt', 'FACOAL184', 'NDPK5m', 'NDPK3n'], inactive_NC:['UMPK2n', 'EX_cys__L_e', 'RADH', 'EX_strdnc_e', 'PROSTGE2t2', 'ORNt3m', 'STRDNCt']\n", + "Zero-expression evidence for reaction...\n", + "2148\n", + "2148\n", + "check_model_function done ....\n", + "Len P: 1314\n", + "num_removed 278\n", + "Len P AFTER 1313\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 278 (37 core, 241 non-core); Num. remaining: 1313\n", + "Reaction no. 49\n", + "Attempting to remove reaction: UMPK7n ...\n", + "Initial PM reactions: 2148\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.274905999999987\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['DCK2n', 'CHOLtu', 'SUCOAS1m'], inactive_NC:['Htx', 'H2Otly', 'EX_cit_e', 'UMPK7n']\n", + "Zero-expression evidence for reaction...\n", + "2148\n", + "2148\n", + "check_model_function done ....\n", + "Len P: 1313\n", + "num_removed 278\n", + "Len P AFTER 1312\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 278 (37 core, 241 non-core); Num. remaining: 1312\n", + "Reaction no. 50\n", + "Attempting to remove reaction: UMPK5n ...\n", + "Initial PM reactions: 2148\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.2684769999999617\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['FACOAL2042'], inactive_NC:['EICOSTETt', 'CITt4_4', 'EX_eicostet_e', 'ORNt3m', 'UMPK5n']\n", + "Zero-expression evidence for reaction...\n", + "2148\n", + "2148\n", + "check_model_function done ....\n", + "PM reactions (before): 2148\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2142\n", + "Num. removed: 284 (38 core, 246 non-core); Num. remaining: 1307\n", + "Reaction no. 51\n", + "Attempting to remove reaction: TYRDOPO ...\n", + "Initial PM reactions: 2142\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.14827200000002\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['DCK1n'], inactive_NC:['TYRDOPO']\n", + "Zero-expression evidence for reaction...\n", + "2142\n", + "2142\n", + "check_model_function done ....\n", + "Len P: 1307\n", + "num_removed 284\n", + "Len P AFTER 1306\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 284 (38 core, 246 non-core); Num. remaining: 1306\n", + "Reaction no. 52\n", + "Attempting to remove reaction: SO4OXAtex2 ...\n", + "Initial PM reactions: 2142\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.007475999999997\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CHOLtu', 'GSNt'], inactive_NC:['PIt7_copy1', 'EX_nrpphr_e', 'ESTRONESt', 'SO4OXAtex2']\n", + "Zero-expression evidence for reaction...\n", + "2142\n", + "2142\n", + "check_model_function done ....\n", + "Len P: 1306\n", + "num_removed 284\n", + "Len P AFTER 1305\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 284 (38 core, 246 non-core); Num. remaining: 1305\n", + "Reaction no. 53\n", + "Attempting to remove reaction: TYR3MO2 ...\n", + "Initial PM reactions: 2142\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.2745740000000296\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['MAN6PI', 'NDPK5n'], inactive_NC:['CYTK11', 'TYR3MO2', 'CYTK8n', 'EX_dopa_e']\n", + "Zero-expression evidence for reaction...\n", + "2142\n", + "2142\n", + "check_model_function done ....\n", + "Len P: 1305\n", + "num_removed 284\n", + "Len P AFTER 1304\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 284 (38 core, 246 non-core); Num. remaining: 1304\n", + "Reaction no. 54\n", + "Attempting to remove reaction: THRGLYexR ...\n", + "Initial PM reactions: 2142\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.1645559999999477\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['MTHFD2m', 'CYTDt', 'PUNP5', 'LALDD'], inactive_NC:['THRGLYexR', 'GLYtm', 'CYTK11n', 'SERGLYexR', 'CYTK2_1', 'HIStN1', 'GLCter']\n", + "Zero-expression evidence for reaction...\n", + "2142\n", + "2142\n", + "check_model_function done ....\n", + "Len P: 1304\n", + "num_removed 284\n", + "Len P AFTER 1303\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 284 (38 core, 246 non-core); Num. remaining: 1303\n", + "Reaction no. 55\n", + "Attempting to remove reaction: BAAT5x ...\n", + "Initial PM reactions: 2142\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 33 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.094908000000032\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 34 , inactive_C: ['SCP3x'], inactive_NC:['DHCHOLESTANATEtm', 'CYSAMO', 'PAN4PP', 'PNTEH', 'EX_ala__D_e', 'HYPTROX', 'XOL7AONEtr', 'P45027A16m', 'LCYSTCBOXL', 'BAAT5x', 'PCRNtm', 'CSNAT2m', 'TAURtcx', 'CRNCAR3tp', 'TDCHOLAte', 'VLCS2p', 'P4507A1r', 'P45027A14m', 'AMPtp', '3SALACBOXL', 'EX_lys__L_e', 'XOL7AH2tm', 'HSD3B7', 'HSD3B7P', 'EX_ura_e', 'NAtx', 'URAt', 'EX_tdchola_e', 'CSNAT3x', 'TDCHOLAtx', 'AKR1C41', 'P45027A15m', 'AKR1D']\n", + "Zero-expression evidence for reaction...\n", + "2142\n", + "2142\n", + "check_model_function done ....\n", + "PM reactions (before): 2142\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2108\n", + "Num. removed: 318 (39 core, 279 non-core); Num. remaining: 1271\n", + "Reaction no. 56\n", + "Attempting to remove reaction: CYTK3n ...\n", + "Initial PM reactions: 2108\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8069900000000416\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['DCK2n'], inactive_NC:['CYTK13n', 'CYTK3n', 'UMPK5', 'ABUTt4_2_r']\n", + "Zero-expression evidence for reaction...\n", + "2108\n", + "2108\n", + "check_model_function done ....\n", + "PM reactions (before): 2108\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2103\n", + "Num. removed: 323 (40 core, 283 non-core); Num. remaining: 1267\n", + "Reaction no. 57\n", + "Attempting to remove reaction: CYTK14n ...\n", + "Initial PM reactions: 2103\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.0761059999999816\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['PUNP5', 'NDPK2n'], inactive_NC:['CYTK14n', 'ALADGLNexR']\n", + "Zero-expression evidence for reaction...\n", + "2103\n", + "2103\n", + "check_model_function done ....\n", + "Len P: 1267\n", + "num_removed 323\n", + "Len P AFTER 1266\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 323 (40 core, 283 non-core); Num. remaining: 1266\n", + "Reaction no. 58\n", + "Attempting to remove reaction: UMPK3 ...\n", + "Initial PM reactions: 2103\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.1764080000000376\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['NDPK3n'], inactive_NC:['CYTK1', 'UMPK3']\n", + "Zero-expression evidence for reaction...\n", + "2103\n", + "2103\n", + "check_model_function done ....\n", + "Len P: 1266\n", + "num_removed 323\n", + "Len P AFTER 1265\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 323 (40 core, 283 non-core); Num. remaining: 1265\n", + "Reaction no. 59\n", + "Attempting to remove reaction: CYTK11n ...\n", + "Initial PM reactions: 2103\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.1060059999999794\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['ALATA_L'], inactive_NC:['UMPK2n', 'UMPK7n', 'CYTK4', 'O2tp', 'CYTK11n']\n", + "Zero-expression evidence for reaction...\n", + "2103\n", + "2103\n", + "check_model_function done ....\n", + "PM reactions (before): 2103\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2097\n", + "Num. removed: 329 (41 core, 288 non-core); Num. remaining: 1262\n", + "Reaction no. 60\n", + "Attempting to remove reaction: CYTK4n ...\n", + "Initial PM reactions: 2097\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8640060000000176\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['NDPK1n', 'PYNP2r', 'CYTDt'], inactive_NC:['PMTCOAtx', 'CYTK4n']\n", + "Zero-expression evidence for reaction...\n", + "2097\n", + "2097\n", + "check_model_function done ....\n", + "Len P: 1262\n", + "num_removed 329\n", + "Len P AFTER 1261\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 329 (41 core, 288 non-core); Num. remaining: 1261\n", + "Reaction no. 61\n", + "Attempting to remove reaction: UMPK2 ...\n", + "Initial PM reactions: 2097\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9111259999999675\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['LALDD', 'NDPK4m'], inactive_NC:['UMPK2', 'ADK3', 'CYTK2n']\n", + "Zero-expression evidence for reaction...\n", + "2097\n", + "2097\n", + "check_model_function done ....\n", + "Len P: 1261\n", + "num_removed 329\n", + "Len P AFTER 1260\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 329 (41 core, 288 non-core); Num. remaining: 1260\n", + "Reaction no. 62\n", + "Attempting to remove reaction: CYTK7 ...\n", + "Initial PM reactions: 2097\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.991724999999974\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['RAI3', 'LEUtec', 'LALDD', 'PUNP5'], inactive_NC:['CYTK12n', 'UMPK3', 'CYTK7']\n", + "Zero-expression evidence for reaction...\n", + "2097\n", + "2097\n", + "check_model_function done ....\n", + "Len P: 1260\n", + "num_removed 329\n", + "Len P AFTER 1259\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 329 (41 core, 288 non-core); Num. remaining: 1259\n", + "Reaction no. 63\n", + "Attempting to remove reaction: UMPK4 ...\n", + "Initial PM reactions: 2097\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.123220999999944\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['UMPK4', 'ABUTt2r', 'CYTK2n']\n", + "Zero-expression evidence for reaction...\n", + "2097\n", + "2097\n", + "check_model_function done ....\n", + "PM reactions (before): 2097\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2094\n", + "Num. removed: 332 (41 core, 291 non-core); Num. remaining: 1256\n", + "Reaction no. 64\n", + "Attempting to remove reaction: 34HPPOR ...\n", + "Initial PM reactions: 2094\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.2828439999999546\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['FUMAC', 'FUM', 'TYRTA', 'MACACI'], inactive_NC:['HGNTOR', 'EX_dgsn_e', 'DGSNt', '10FTHFtm', '34HPPOR']\n", + "Zero-expression evidence for reaction...\n", + "2094\n", + "2094\n", + "check_model_function done ....\n", + "Len P: 1256\n", + "num_removed 332\n", + "Len P AFTER 1255\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 332 (41 core, 291 non-core); Num. remaining: 1255\n", + "Reaction no. 65\n", + "Attempting to remove reaction: ALADGLNexR ...\n", + "Initial PM reactions: 2094\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8074400000000423\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GALt1r'], inactive_NC:['ALADGLNexR']\n", + "Zero-expression evidence for reaction...\n", + "2094\n", + "2094\n", + "check_model_function done ....\n", + "Len P: 1255\n", + "num_removed 332\n", + "Len P AFTER 1254\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 332 (41 core, 291 non-core); Num. remaining: 1254\n", + "Reaction no. 66\n", + "Attempting to remove reaction: THRD_L ...\n", + "Initial PM reactions: 2094\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9211290000000645\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['NDPK7m'], inactive_NC:['THRD_L']\n", + "Zero-expression evidence for reaction...\n", + "2094\n", + "2094\n", + "check_model_function done ....\n", + "Len P: 1254\n", + "num_removed 332\n", + "Len P AFTER 1253\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 332 (41 core, 291 non-core); Num. remaining: 1253\n", + "Reaction no. 67\n", + "Attempting to remove reaction: CSNATp ...\n", + "Initial PM reactions: 2094\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 51 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.393083000000047\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 52 , inactive_C: ['ARACHCPT2', 'ARACHCPT1', 'FAOXC226205m', 'CYTDt', 'ARACHCRNt', 'FAOXC226', 'HMGLx', 'C226CPT1', 'C226CPT2', 'FAOXC200180m', 'NDPK7m'], inactive_NC:['FAOXC2452253x', 'ARTFR207', 'FAOXC2442246x', 'C226CRNt', 'FAOXC18480x', 'FAOXC2242046x', 'FAOXC180x', 'ARACHCOAtx', 'LGNCCOAtx', 'ARTFR213', 'TETPENT6COAtx', 'ARACHDCOAtx', 'C226COAtx', 'EX_gua_e', 'FAOXC200180x', 'FAOXC2251836x', 'DESAT22_2p', 'FAOXC260240x', 'FAOXC2452256x', 'NRVNCCOAtx', 'FAOXC246226x', 'OCCOAtx', 'GUAt', 'ACACtx', 'TMNDNCCOAtx', 'CSNATp', 'FAOXC2252053x', 'ARTFR51', 'TETPENT3COAtx', 'FAOXC2051843x', 'HEXCCOAtx', 'FAOXC240200x', 'FAOXC241181x', 'MTHFD2i', 'FAOXC16080x', 'TETHEX3COAtx', 'FAOXC183806x', 'ODECOAtx', 'FAOXC226205x', 'TETTET6COAtx', 'CRNCARtp']\n", + "Zero-expression evidence for reaction...\n", + "2094\n", + "2094\n", + "check_model_function done ....\n", + "PM reactions (before): 2094\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2042\n", + "Num. removed: 384 (52 core, 332 non-core); Num. remaining: 1213\n", + "Reaction no. 68\n", + "Attempting to remove reaction: CYSTSERex ...\n", + "Initial PM reactions: 2042\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.057197999999971\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PUNP4'], inactive_NC:['CYSTSERex', 'ADK3']\n", + "Zero-expression evidence for reaction...\n", + "2042\n", + "2042\n", + "check_model_function done ....\n", + "Len P: 1213\n", + "num_removed 384\n", + "Len P AFTER 1212\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 384 (52 core, 332 non-core); Num. remaining: 1212\n", + "Reaction no. 69\n", + "Attempting to remove reaction: CYSGLYex_copy1 ...\n", + "Initial PM reactions: 2042\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9877900000000182\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['PUNP4', 'LALDD', 'FACOAL246_1'], inactive_NC:['EX_tethex3_e', 'UMPK3', 'CYSGLYex_copy1', 'TETHEX3t']\n", + "Zero-expression evidence for reaction...\n", + "2042\n", + "2042\n", + "check_model_function done ....\n", + "Len P: 1212\n", + "num_removed 384\n", + "Len P AFTER 1211\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 384 (52 core, 332 non-core); Num. remaining: 1211\n", + "Reaction no. 70\n", + "Attempting to remove reaction: CYSGLYex_copy2 ...\n", + "Initial PM reactions: 2042\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6882490000000416\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['CYSGLYex_copy2', 'EX_meoh_e', 'MEOHt2']\n", + "Zero-expression evidence for reaction...\n", + "2042\n", + "2042\n", + "check_model_function done ....\n", + "PM reactions (before): 2042\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2039\n", + "Num. removed: 387 (52 core, 335 non-core); Num. remaining: 1208\n", + "Reaction no. 71\n", + "Attempting to remove reaction: THRGLNexR ...\n", + "Initial PM reactions: 2039\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 12 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.709081000000083\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 13 , inactive_C: ['2HBO', 'FACOAL203', 'MAN6PI', '2HBt2', 'ACACt2m'], inactive_NC:['CYTK2', 'DLNLCGt', 'SERGLYexR', 'EX_dlnlcg_e', 'THRGLNexR', 'ESTRONESt', 'EX_2hb_e', 'HMGCOAtm']\n", + "Zero-expression evidence for reaction...\n", + "2039\n", + "2039\n", + "check_model_function done ....\n", + "Len P: 1208\n", + "num_removed 387\n", + "Len P AFTER 1207\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 387 (52 core, 335 non-core); Num. remaining: 1207\n", + "Reaction no. 72\n", + "Attempting to remove reaction: GLYCTO1p ...\n", + "Initial PM reactions: 2039\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.1337859999999864\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['GCALDD', 'FBA4', 'GLXO1', 'GLYCLTDy'], inactive_NC:['GLXO2p', 'GLYCTO1p', 'GLYCLTtp', 'OXAtp', 'KHK2', 'EX_oxa_e', 'GLXtp']\n", + "Zero-expression evidence for reaction...\n", + "2039\n", + "2039\n", + "check_model_function done ....\n", + "Len P: 1207\n", + "num_removed 387\n", + "Len P AFTER 1206\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 387 (52 core, 335 non-core); Num. remaining: 1206\n", + "Reaction no. 73\n", + "Attempting to remove reaction: ACOAO7p ...\n", + "Initial PM reactions: 2039\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.082409000000098\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['C161CRN2t', 'FAOXC161802m', 'C161CPT22', 'COAtim', 'C161CPT12'], inactive_NC:['ACOAO7p', 'HDD2COAtx', 'ARTFR61', 'RTOT6', 'PMTCOAtx']\n", + "Zero-expression evidence for reaction...\n", + "2039\n", + "2039\n", + "check_model_function done ....\n", + "Len P: 1206\n", + "num_removed 387\n", + "Len P AFTER 1205\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 387 (52 core, 335 non-core); Num. remaining: 1205\n", + "Reaction no. 74\n", + "Attempting to remove reaction: SERGLYexR ...\n", + "Initial PM reactions: 2039\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.112107999999921\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['FACOAL246_1'], inactive_NC:['EX_tethex3_e', 'TETHEX3t', 'SERGLYexR', 'EX_cytd_e']\n", + "Zero-expression evidence for reaction...\n", + "2039\n", + "2039\n", + "check_model_function done ....\n", + "PM reactions (before): 2039\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2034\n", + "Num. removed: 392 (53 core, 339 non-core); Num. remaining: 1201\n", + "Reaction no. 75\n", + "Attempting to remove reaction: SPODMe ...\n", + "Initial PM reactions: 2034\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.806163999999967\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['FACOAL2251'], inactive_NC:['SPODMe', 'DCSPTN1t', 'EX_dcsptn1_e']\n", + "Zero-expression evidence for reaction...\n", + "2034\n", + "2034\n", + "check_model_function done ....\n", + "PM reactions (before): 2034\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2030\n", + "Num. removed: 396 (54 core, 342 non-core); Num. remaining: 1198\n", + "Reaction no. 76\n", + "Attempting to remove reaction: UDPG4E ...\n", + "Initial PM reactions: 2030\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 60 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.402692000000002\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 61 , inactive_C: ['UDPDOLPT_U', 'GLDBRAN', 'GGNG', 'GBA', 'GALKr', 'UDPDOLPT_L', 'GLGNS1', 'NACHEX27ly', 'UGCG', 'GLCURtly', 'CERT1rt', 'GLCAASE8ly', 'GLPASE2', 'GASNASEly', 'GLBRAN', 'GLPASE1', 'UGLT', 'UDPGD', 'GLCAASE9ly', 'FUCASEe', 'ASAH1', 'SIAASEly', 'GALASE1ly', 'CERT2rt', 'AHEXASEly', 'ACNAMlt'], inactive_NC:['DOLPH_Ler', 'ENGASEly', 'HAS2', 'DOLGPP_Uer', 'DOLGLCP_Uter', 'DOLP_Uter', 'NDP7er', 'LACZe', 'DOLICHOL_Uter', 'HAtly', 'ADK3', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GUR1PP', 'UDPG4E', 'CHOLPtl', 'GALtly', 'DOLP_Lter', 'UDPG1P', 'SPHINGStl', 'DOLK_U', 'EX_s2l2fn2m2masn_e', 'DOLGLCP_Lter', 'EX_vitd3_e', 'ATPasel', 'EX_lcts_e', 'Rtotaltl', 'UDPGLCter', 'SPHMYLNtl', 'UDPGNP', 'DOLPH_Uer', 'DOLK_L', 'HAS1', 'SMPD3l']\n", + "Zero-expression evidence for reaction...\n", + "2030\n", + "2030\n", + "check_model_function done ....\n", + "Len P: 1198\n", + "num_removed 396\n", + "Len P AFTER 1197\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 396 (54 core, 342 non-core); Num. remaining: 1197\n", + "Reaction no. 77\n", + "Attempting to remove reaction: CLOHtex2 ...\n", + "Initial PM reactions: 2030\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.051198999999997\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PUNP4'], inactive_NC:['CLOHtex2', 'PROt2r']\n", + "Zero-expression evidence for reaction...\n", + "2030\n", + "2030\n", + "check_model_function done ....\n", + "Len P: 1197\n", + "num_removed 396\n", + "Len P AFTER 1196\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 396 (54 core, 342 non-core); Num. remaining: 1196\n", + "Reaction no. 78\n", + "Attempting to remove reaction: CLFORtex2 ...\n", + "Initial PM reactions: 2030\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.047490000000039\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['DCMPDA', 'LEUtec'], inactive_NC:['CLFORtex2', 'PROt4_2_r', 'ESTRONESt']\n", + "Zero-expression evidence for reaction...\n", + "2030\n", + "2030\n", + "check_model_function done ....\n", + "Len P: 1196\n", + "num_removed 396\n", + "Len P AFTER 1195\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 396 (54 core, 342 non-core); Num. remaining: 1195\n", + "Reaction no. 79\n", + "Attempting to remove reaction: DALAOXx ...\n", + "Initial PM reactions: 2030\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 13 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6186330000000453\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 14 , inactive_C: ['PUNP5', 'NDPK4m', 'LALDD', 'NDPK1', 'MTHFD2m', 'PYNP2r', 'ALAR', 'URIt', 'PUNP2', 'PYRt2p'], inactive_NC:['CYTK8', 'DALAxt', 'DALAOXx', 'ALADGLYexR']\n", + "Zero-expression evidence for reaction...\n", + "2030\n", + "2030\n", + "check_model_function done ....\n", + "Len P: 1195\n", + "num_removed 396\n", + "Len P AFTER 1194\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 396 (54 core, 342 non-core); Num. remaining: 1194\n", + "Reaction no. 80\n", + "Attempting to remove reaction: CYTK2_1 ...\n", + "Initial PM reactions: 2030\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7201090000000931\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GALt1r'], inactive_NC:['CYTK2_1', 'CYTK9', 'ADK3', 'UMPK2']\n", + "Zero-expression evidence for reaction...\n", + "2030\n", + "2030\n", + "check_model_function done ....\n", + "PM reactions (before): 2030\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2025\n", + "Num. removed: 401 (55 core, 346 non-core); Num. remaining: 1191\n", + "Reaction no. 81\n", + "Attempting to remove reaction: PEPCK_re ...\n", + "Initial PM reactions: 2025\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8849969999998848\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['GSNt'], inactive_NC:['UMPK3', 'PEPCK_re', 'EX_cys__L_e', '10FTHFtm', 'ESTRONESt']\n", + "Zero-expression evidence for reaction...\n", + "2025\n", + "2025\n", + "check_model_function done ....\n", + "PM reactions (before): 2025\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2019\n", + "Num. removed: 407 (56 core, 351 non-core); Num. remaining: 1187\n", + "Reaction no. 82\n", + "Attempting to remove reaction: ACOAD8m ...\n", + "Initial PM reactions: 2019\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.097590999999966\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['MGCHrm', 'OIVD1m'], inactive_NC:['ALADGLNexR', 'ACOAD8m', 'CYTK7', 'MCCCrm', 'GLCter']\n", + "Zero-expression evidence for reaction...\n", + "2019\n", + "2019\n", + "check_model_function done ....\n", + "Len P: 1187\n", + "num_removed 407\n", + "Len P AFTER 1186\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 407 (56 core, 351 non-core); Num. remaining: 1186\n", + "Reaction no. 83\n", + "Attempting to remove reaction: DHORD9 ...\n", + "Initial PM reactions: 2019\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7603670000000875\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['OMPDC', 'LALDD', 'ORPT'], inactive_NC:['CBPS', 'DHORD9', 'ASPCT', 'DHORTS']\n", + "Zero-expression evidence for reaction...\n", + "2019\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2019\n", + "check_model_function done ....\n", + "Len P: 1186\n", + "num_removed 407\n", + "Len P AFTER 1185\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 407 (56 core, 351 non-core); Num. remaining: 1185\n", + "Reaction no. 84\n", + "Attempting to remove reaction: PROSTGD2t ...\n", + "Initial PM reactions: 2019\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.0603869999999915\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['NDPK3', 'PUNP4', 'MAN6PI', 'PGS'], inactive_NC:['EX_prostgd2_e', 'PROSTGD2t', 'CYTK12n', 'PROSTGE2t2', 'PGDI', 'CYTK10']\n", + "Zero-expression evidence for reaction...\n", + "2019\n", + "2019\n", + "check_model_function done ....\n", + "Len P: 1185\n", + "num_removed 407\n", + "Len P AFTER 1184\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 407 (56 core, 351 non-core); Num. remaining: 1184\n", + "Reaction no. 85\n", + "Attempting to remove reaction: BILDGLCURt ...\n", + "Initial PM reactions: 2019\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.996786999999813\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['NDPK3'], inactive_NC:['BILDGLCURt']\n", + "Zero-expression evidence for reaction...\n", + "2019\n", + "2019\n", + "check_model_function done ....\n", + "Len P: 1184\n", + "num_removed 407\n", + "Len P AFTER 1183\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 407 (56 core, 351 non-core); Num. remaining: 1183\n", + "Reaction no. 86\n", + "Attempting to remove reaction: LEUKTRC4t ...\n", + "Initial PM reactions: 2019\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 18 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6468869999998788\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 19 , inactive_C: ['ASNtN1', 'LTC4Sr', 'LALDD', 'DURIPP', 'NDPK3'], inactive_NC:['LEUKTRC4t', 'GTHRDtr', 'LEUKTRD4tr', 'CYTK13', 'LEUKTRA4tr', 'ALOX5', 'GLUtr', 'LTD4DP', 'GGT5r', 'NRPPHRtu', 'LTC4CP', 'EX_leuktrC4_e', 'ALOX52', 'GGT6']\n", + "Zero-expression evidence for reaction...\n", + "2019\n", + "2019\n", + "check_model_function done ....\n", + "Len P: 1183\n", + "num_removed 407\n", + "Len P AFTER 1182\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 407 (56 core, 351 non-core); Num. remaining: 1182\n", + "Reaction no. 87\n", + "Attempting to remove reaction: GTMLTe ...\n", + "Initial PM reactions: 2019\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 15 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.954757999999856\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 16 , inactive_C: ['PUNP5', 'LALDD', 'MTHFD2m', 'MAN6PI', 'PUNP2', 'FACOAL203'], inactive_NC:['GHMT2r', 'CYTK7', 'CYTK2', 'GGLUCT', 'DLNLCGt', 'GTMLTe', 'H2O2t', 'EX_dlnlcg_e', 'ALADGLYexR', 'OPAH']\n", + "Zero-expression evidence for reaction...\n", + "2019\n", + "2019\n", + "check_model_function done ....\n", + "Len P: 1182\n", + "num_removed 407\n", + "Len P AFTER 1181\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 407 (56 core, 351 non-core); Num. remaining: 1181\n", + "Reaction no. 88\n", + "Attempting to remove reaction: CLOXAtex2 ...\n", + "Initial PM reactions: 2019\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.758670999999822\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['FACOAL203'], inactive_NC:['CLOXAtex2', 'EX_dlnlcg_e', 'DLNLCGt']\n", + "Zero-expression evidence for reaction...\n", + "2019\n", + "2019\n", + "check_model_function done ....\n", + "PM reactions (before): 2019\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2015\n", + "Num. removed: 411 (57 core, 354 non-core); Num. remaining: 1178\n", + "Reaction no. 89\n", + "Attempting to remove reaction: PROSTGE1t ...\n", + "Initial PM reactions: 2015\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7207780000001094\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['ASPTA', 'PROSTGE1t3'], inactive_NC:['PROSTGE1t']\n", + "Zero-expression evidence for reaction...\n", + "2015\n", + "2015\n", + "check_model_function done ....\n", + "Len P: 1178\n", + "num_removed 411\n", + "Len P AFTER 1177\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 411 (57 core, 354 non-core); Num. remaining: 1177\n", + "Reaction no. 90\n", + "Attempting to remove reaction: BILIRUBt2 ...\n", + "Initial PM reactions: 2015\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 54 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.2940770000000157\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 55 , inactive_C: ['HOXG', 'BILIRED', 'UGT1A10r', 'PPPGOm', 'UGT1A5r', 'ALASm', 'UGT1A1r', 'HMBS', 'CPPPGO', 'ESTRADIOLGLCt2', 'UPPDC1', 'URIt', 'UGT1A2r', 'UPP3S', 'UGT1A5r2', 'UGT1A6r'], inactive_NC:['BILIRUBt2', 'RETNtr', 'RETNGLCt2', 'BILGLCURte', 'EX_estradiolglc_e', 'EX_dgsn_e', 'BILGLCURtr', 'BILIRUBtr', 'COt', 'EX_retnglc_e', 'ESTRONEGLCt', '5ADTSTSTERONEGLCtr', '5AOPtm', 'PPBNGS', 'EX_estroneglc_e', 'EX_13_cis_retnglc_e', 'DGSNt', 'FCLTm', 'UGT1A9r', '5ADTSTSTERONEtr', 'ESTRONEGLCtr', 'CYTK7', 'NRPPHRtu', 'PHEMEtm', 'BILDGLCURtr', 'RETNGLCt', 'RETNtr2', 'RETNGLCtr', 'RETNGLCt2r', 'EX_co_e', 'EX_bildglcur_e', '5ADTSTSTERONEGLCte', 'ESTRADIOLGLCtr', 'EX_bilirub_e', 'PPPG9tm', 'It', 'EX_bilglcur_e', 'FE2tm', 'EX_5adtststeroneglc_e']\n", + "Zero-expression evidence for reaction...\n", + "2015\n", + "2015\n", + "check_model_function done ....\n", + "Len P: 1177\n", + "num_removed 411\n", + "Len P AFTER 1176\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 411 (57 core, 354 non-core); Num. remaining: 1176\n", + "Reaction no. 91\n", + "Attempting to remove reaction: GUAPRT ...\n", + "Initial PM reactions: 2015\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.028471999999965\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['NDPK2'], inactive_NC:['GUAPRT']\n", + "Zero-expression evidence for reaction...\n", + "2015\n", + "2015\n", + "check_model_function done ....\n", + "Len P: 1176\n", + "num_removed 411\n", + "Len P AFTER 1175\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 411 (57 core, 354 non-core); Num. remaining: 1175\n", + "Reaction no. 92\n", + "Attempting to remove reaction: HXPRT ...\n", + "Initial PM reactions: 2015\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.028586000000132\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['PUNP2'], inactive_NC:['HXPRT', 'EX_nrpphr_e', 'EX_asn__L_e']\n", + "Zero-expression evidence for reaction...\n", + "2015\n", + "2015\n", + "check_model_function done ....\n", + "PM reactions (before): 2015\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2011\n", + "Num. removed: 415 (58 core, 357 non-core); Num. remaining: 1172\n", + "Reaction no. 93\n", + "Attempting to remove reaction: ALAGLNexR ...\n", + "Initial PM reactions: 2011\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5851120000002084\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['DURIPP', 'L_LACt2r'], inactive_NC:['CYTK12n', 'ALAGLNexR', 'EX_retfa_e']\n", + "Zero-expression evidence for reaction...\n", + "2011\n", + "2011\n", + "check_model_function done ....\n", + "Len P: 1172\n", + "num_removed 415\n", + "Len P AFTER 1171\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 415 (58 core, 357 non-core); Num. remaining: 1171\n", + "Reaction no. 94\n", + "Attempting to remove reaction: CYTK12 ...\n", + "Initial PM reactions: 2011\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6877749999998741\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['FACOAL1813'], inactive_NC:['CYTK12', 'ELAIDt', 'EX_elaid_e']\n", + "Zero-expression evidence for reaction...\n", + "2011\n", + "2011\n", + "check_model_function done ....\n", + "PM reactions (before): 2011\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2007\n", + "Num. removed: 419 (59 core, 360 non-core); Num. remaining: 1168\n", + "Reaction no. 95\n", + "Attempting to remove reaction: CYSGLUexR ...\n", + "Initial PM reactions: 2007\n", + "check_model_function done ....\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7635310000000572\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['CYSGLUexR']\n", + "Zero-expression evidence for reaction...\n", + "2007\n", + "2007\n", + "check_model_function done ....\n", + "PM reactions (before): 2007\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2006\n", + "Num. removed: 420 (59 core, 361 non-core); Num. remaining: 1167\n", + "Reaction no. 96\n", + "Attempting to remove reaction: GLXO2p ...\n", + "Initial PM reactions: 2006\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7217219999999998\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['GLXO2p', 'OXAtp']\n", + "Zero-expression evidence for reaction...\n", + "2006\n", + "2006\n", + "check_model_function done ....\n", + "PM reactions (before): 2006\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2004\n", + "Num. removed: 422 (59 core, 363 non-core); Num. remaining: 1165\n", + "Reaction no. 97\n", + "Attempting to remove reaction: SO4CLtex2 ...\n", + "Initial PM reactions: 2004\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.047416999999996\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['NDPK3', 'SERtN1', 'ADNt', 'MAN6PI'], inactive_NC:['SO4CLtex2']\n", + "Zero-expression evidence for reaction...\n", + "2004\n", + "2004\n", + "check_model_function done ....\n", + "Len P: 1165\n", + "num_removed 422\n", + "Len P AFTER 1164\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 422 (59 core, 363 non-core); Num. remaining: 1164\n", + "Reaction no. 98\n", + "Attempting to remove reaction: SARDHm ...\n", + "Initial PM reactions: 2004\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7349139999998897\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['NDPK3', 'MTHFCm', 'URIt'], inactive_NC:['SARCStm', 'SARCStex', 'SARDHm', 'GNMT', 'EX_sarcs_e']\n", + "Zero-expression evidence for reaction...\n", + "2004\n", + "2004\n", + "check_model_function done ....\n", + "Len P: 1164\n", + "num_removed 422\n", + "Len P AFTER 1163\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 422 (59 core, 363 non-core); Num. remaining: 1163\n", + "Reaction no. 99\n", + "Attempting to remove reaction: VALTA ...\n", + "Initial PM reactions: 2004\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7423349999999118\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['LALDD'], inactive_NC:['VALTA', '3MOBt2im', 'CYTK7']\n", + "Zero-expression evidence for reaction...\n", + "2004\n", + "2004\n", + "check_model_function done ....\n", + "PM reactions (before): 2004\n", + "Removed all inactive reactions\n", + "PM reactions (after): 2000\n", + "Num. removed: 426 (60 core, 366 non-core); Num. remaining: 1161\n", + "Reaction no. 100\n", + "Attempting to remove reaction: CYTK8 ...\n", + "Initial PM reactions: 2000\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6936149999999088\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['NDPK3', 'CYStec'], inactive_NC:['CYTK8', 'CYTK11', 'EX_h2o2_e', 'NRPPHRtu', 'CYTK10']\n", + "Zero-expression evidence for reaction...\n", + "2000\n", + "2000\n", + "check_model_function done ....\n", + "Len P: 1161\n", + "num_removed 426\n", + "Len P AFTER 1160\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 426 (60 core, 366 non-core); Num. remaining: 1160\n", + "Reaction no. 101\n", + "Attempting to remove reaction: UREAtm ...\n", + "Initial PM reactions: 2000\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7087859999999182\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['ARGNm', 'CBPSam'], inactive_NC:['CITRtm', 'UREAtm', 'ARGtm', 'OCBTm']\n", + "Zero-expression evidence for reaction...\n", + "2000\n", + "2000\n", + "check_model_function done ....\n", + "Len P: 1160\n", + "num_removed 426\n", + "Len P AFTER 1159\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 426 (60 core, 366 non-core); Num. remaining: 1159\n", + "Reaction no. 102\n", + "Attempting to remove reaction: CYTDn ...\n", + "Initial PM reactions: 2000\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7396519999999782\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: [], inactive_NC:['Uritn', 'CYTDn', 'CYTDtn', 'CYTK12n']\n", + "Zero-expression evidence for reaction...\n", + "2000\n", + "2000\n", + "check_model_function done ....\n", + "PM reactions (before): 2000\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1996\n", + "Num. removed: 430 (60 core, 370 non-core); Num. remaining: 1156\n", + "Reaction no. 103\n", + "Attempting to remove reaction: DCYTDn ...\n", + "Initial PM reactions: 1996\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.825313000000051\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['DCK1n'], inactive_NC:['DCYTDn', 'NH4tn', 'DURItn']\n", + "Zero-expression evidence for reaction...\n", + "1996\n", + "1996\n", + "check_model_function done ....\n", + "PM reactions (before): 1996\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1992\n", + "Num. removed: 434 (61 core, 373 non-core); Num. remaining: 1153\n", + "Reaction no. 104\n", + "Attempting to remove reaction: GCPNn ...\n", + "Initial PM reactions: 1992\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7160260000000562\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['DURIPP'], inactive_NC:['35CGMPtn', 'GMPtn', 'H2Otly', 'GCPNn']\n", + "Zero-expression evidence for reaction...\n", + "1992\n", + "1992\n", + "check_model_function done ....\n", + "PM reactions (before): 1992\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1987\n", + "Num. removed: 439 (62 core, 377 non-core); Num. remaining: 1149\n", + "Reaction no. 105\n", + "Attempting to remove reaction: PI4PLCn ...\n", + "Initial PM reactions: 1987\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8009389999999712\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['LDH_L', 'NDPK3', 'COAtim'], inactive_NC:['EX_dopa_e', 'MI14Ptn', 'PI4PLCn']\n", + "Zero-expression evidence for reaction...\n", + "1987\n", + "1987\n", + "check_model_function done ....\n", + "Len P: 1149\n", + "num_removed 439\n", + "Len P AFTER 1148\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 439 (62 core, 377 non-core); Num. remaining: 1148\n", + "Reaction no. 106\n", + "Attempting to remove reaction: PIPLCn ...\n", + "Initial PM reactions: 1987\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9996549999998479\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['MAN6PI', 'NDPK4m'], inactive_NC:['MI1P_Dtn', 'PIPLCn', 'ALAGLNexR']\n", + "Zero-expression evidence for reaction...\n", + "1987\n", + "1987\n", + "check_model_function done ....\n", + "Len P: 1148\n", + "num_removed 439\n", + "Len P AFTER 1147\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 439 (62 core, 377 non-core); Num. remaining: 1147\n", + "Reaction no. 107\n", + "Attempting to remove reaction: CYTK10 ...\n", + "Initial PM reactions: 1987\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9941329999999198\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['COAtim'], inactive_NC:['CYTK10']\n", + "Zero-expression evidence for reaction...\n", + "1987\n", + "1987\n", + "check_model_function done ....\n", + "Len P: 1147\n", + "num_removed 439\n", + "Len P AFTER 1146\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 439 (62 core, 377 non-core); Num. remaining: 1146\n", + "Reaction no. 108\n", + "Attempting to remove reaction: CRNt_copy2 ...\n", + "Initial PM reactions: 1987\n", + "check_model_function done ....\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7254339999999502\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['CRNt_copy2']\n", + "Zero-expression evidence for reaction...\n", + "1987\n", + "1987\n", + "check_model_function done ....\n", + "PM reactions (before): 1987\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1986\n", + "Num. removed: 440 (62 core, 378 non-core); Num. remaining: 1145\n", + "Reaction no. 109\n", + "Attempting to remove reaction: GND ...\n", + "Initial PM reactions: 1986\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7083299999999326\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['FTHFLi', 'ADNt', 'SERtN1', 'RPI', 'MAN6PI', 'COAtim', 'G6PDH2r'], inactive_NC:['PGL', 'CYTK11', 'GND', 'EX_hco3_e', 'ALADGLYexR']\n", + "Zero-expression evidence for reaction...\n", + "1986\n", + "1986\n", + "check_model_function done ....\n", + "Len P: 1145\n", + "num_removed 440\n", + "Len P AFTER 1144\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 440 (62 core, 378 non-core); Num. remaining: 1144\n", + "Reaction no. 110\n", + "Attempting to remove reaction: CITL ...\n", + "Initial PM reactions: 1986\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7384550000001582\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['NDPK6m', 'ASPTA'], inactive_NC:['FTHFLmi', 'ALADGLNexR', 'ALAGLNexR', 'H2O2t', 'CITL', 'NRPPHRtu', 'FORtm']\n", + "Zero-expression evidence for reaction...\n", + "1986\n", + "1986\n", + "check_model_function done ....\n", + "PM reactions (before): 1986\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1977\n", + "Num. removed: 449 (64 core, 385 non-core); Num. remaining: 1139\n", + "Reaction no. 111\n", + "Attempting to remove reaction: PTE3x ...\n", + "Initial PM reactions: 1977\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.703358999999864\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['PRISTCOAtx', 'PRISTtx', 'GLCter', 'FACOAL191', 'PTE3x']\n", + "Zero-expression evidence for reaction...\n", + "1977\n", + "1977\n", + "check_model_function done ....\n", + "PM reactions (before): 1977\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1972\n", + "Num. removed: 454 (64 core, 390 non-core); Num. remaining: 1134\n", + "Reaction no. 112\n", + "Attempting to remove reaction: ALOX52 ...\n", + "Initial PM reactions: 1972\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 15 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.0431109999999535\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 16 , inactive_C: ['LTC4Sr', 'ACACt2m'], inactive_NC:['LEUKTRC4t', 'GTHRDtr', 'LEUKTRD4tr', 'EX_dgsn_e', 'GLUtr', 'LTD4DP', 'GGT5r', 'LTC4CP', 'EX_leuktrC4_e', 'GGT6', 'LEUKTRA4tr', 'ALOX5', 'DGSNt', 'ALOX52']\n", + "Zero-expression evidence for reaction...\n", + "1972\n", + "1972\n", + "check_model_function done ....\n", + "PM reactions (before): 1972\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1956\n", + "Num. removed: 470 (66 core, 404 non-core); Num. remaining: 1122\n", + "Reaction no. 113\n", + "Attempting to remove reaction: CLHCO3tex2 ...\n", + "Initial PM reactions: 1956\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.928955999999971\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['NDPK3', 'LEUtec', 'FACOAL184'], inactive_NC:['STRDNCt', 'EX_strdnc_e', 'CLHCO3tex2']\n", + "Zero-expression evidence for reaction...\n", + "1956\n", + "1956\n", + "check_model_function done ....\n", + "Len P: 1122\n", + "num_removed 470\n", + "Len P AFTER 1121\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 470 (66 core, 404 non-core); Num. remaining: 1121\n", + "Reaction no. 114\n", + "Attempting to remove reaction: PRDX ...\n", + "Initial PM reactions: 1956\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8719280000000253\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['PUNP4', 'DCMPDA'], inactive_NC:['DOPAt4_2_r', 'PROt4_2_r', 'DURIt', 'EX_duri_e', 'PRDX']\n", + "Zero-expression evidence for reaction...\n", + "1956\n", + "1956\n", + "check_model_function done ....\n", + "Len P: 1121\n", + "num_removed 470\n", + "Len P AFTER 1120\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 470 (66 core, 404 non-core); Num. remaining: 1120\n", + "Reaction no. 115\n", + "Attempting to remove reaction: UMPK7 ...\n", + "Initial PM reactions: 1956\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5940610000000106\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['PUNP4'], inactive_NC:['UMPK7']\n", + "Zero-expression evidence for reaction...\n", + "1956\n", + "1956\n", + "check_model_function done ....\n", + "Len P: 1120\n", + "num_removed 470\n", + "Len P AFTER 1119\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 470 (66 core, 404 non-core); Num. remaining: 1119\n", + "Reaction no. 116\n", + "Attempting to remove reaction: FBA5 ...\n", + "Initial PM reactions: 1956\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7504810000000361\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['ADNt'], inactive_NC:['H2CO3Dm', 'FBA5', 'TAGAT_Dt', 'KHK3', 'H2CO3D2m', 'DURIt', 'EX_duri_e', 'EX_tag__D_e', 'PCt']\n", + "Zero-expression evidence for reaction...\n", + "1956\n", + "1956\n", + "check_model_function done ....\n", + "PM reactions (before): 1956\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1946\n", + "Num. removed: 480 (67 core, 413 non-core); Num. remaining: 1110\n", + "Reaction no. 117\n", + "Attempting to remove reaction: CYTK1 ...\n", + "Initial PM reactions: 1946\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5889299999998912\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['PUNP1', '2HBt2', '2HBO'], inactive_NC:['CYTK1', 'CYTK10', 'EX_2hb_e']\n", + "Zero-expression evidence for reaction...\n", + "1946\n", + "1946\n", + "check_model_function done ....\n", + "Len P: 1110\n", + "num_removed 480\n", + "Len P AFTER 1109\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 480 (67 core, 413 non-core); Num. remaining: 1109\n", + "Reaction no. 118\n", + "Attempting to remove reaction: BTNPLm ...\n", + "Initial PM reactions: 1946\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7214500000000044\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['KCCt', 'PUNP4'], inactive_NC:['BACCLm', 'BTNDm', 'CYTK11', 'EX_chol_e', 'APOC_LYS_BTNPm', 'APOCFm', 'BTNPLm']\n", + "Zero-expression evidence for reaction...\n", + "1946\n", + "1946\n", + "check_model_function done ....\n", + "PM reactions (before): 1946\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1937\n", + "Num. removed: 489 (69 core, 420 non-core); Num. remaining: 1102\n", + "Reaction no. 119\n", + "Attempting to remove reaction: CYTK13 ...\n", + "Initial PM reactions: 1937\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8525200000001405\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['FTHFLi', 'ACACt2', 'L_LACtm'], inactive_NC:['EX_retfa_e', 'CYTK13', 'ADEt', 'EX_acac_e', 'It', 'EX_ade_e']\n", + "Zero-expression evidence for reaction...\n", + "1937\n", + "1937\n", + "check_model_function done ....\n", + "Len P: 1102\n", + "num_removed 489\n", + "Len P AFTER 1101\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 489 (69 core, 420 non-core); Num. remaining: 1101\n", + "Reaction no. 120\n", + "Attempting to remove reaction: ASNNm ...\n", + "Initial PM reactions: 1937\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.0108209999998508\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['LEUtec', 'GDHm'], inactive_NC:['EX_gln__L_e', 'ASNNm', 'ASNtm', 'It']\n", + "Zero-expression evidence for reaction...\n", + "1937\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1937\n", + "check_model_function done ....\n", + "Len P: 1101\n", + "num_removed 489\n", + "Len P AFTER 1100\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 489 (69 core, 420 non-core); Num. remaining: 1100\n", + "Reaction no. 121\n", + "Attempting to remove reaction: NACASPAH ...\n", + "Initial PM reactions: 1937\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.0389880000000176\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['NDPK3', 'DCMPDA'], inactive_NC:['ASPNATm', 'NACASPAH', 'NACASPtm', 'EX_retfa_e']\n", + "Zero-expression evidence for reaction...\n", + "1937\n", + "1937\n", + "check_model_function done ....\n", + "Len P: 1100\n", + "num_removed 489\n", + "Len P AFTER 1099\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 489 (69 core, 420 non-core); Num. remaining: 1099\n", + "Reaction no. 122\n", + "Attempting to remove reaction: HSD3A1r ...\n", + "Initial PM reactions: 1937\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9921889999998257\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['GLCt1', 'HSD17B9r'], inactive_NC:['HSD3B2r', 'HSD3B3r', 'HSD3A1r', 'EX_retfa_e']\n", + "Zero-expression evidence for reaction...\n", + "1937\n", + "1937\n", + "check_model_function done ....\n", + "Len P: 1099\n", + "num_removed 489\n", + "Len P AFTER 1098\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 489 (69 core, 420 non-core); Num. remaining: 1098\n", + "Reaction no. 123\n", + "Attempting to remove reaction: NTD1m ...\n", + "Initial PM reactions: 1937\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9361549999998715\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['DURIK1m', 'RDH1a', 'NKCCt'], inactive_NC:['NTD1m', 'CYTK13']\n", + "Zero-expression evidence for reaction...\n", + "1937\n", + "1937\n", + "check_model_function done ....\n", + "Len P: 1098\n", + "num_removed 489\n", + "Len P AFTER 1097\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 489 (69 core, 420 non-core); Num. remaining: 1097\n", + "Reaction no. 124\n", + "Attempting to remove reaction: NTD5m ...\n", + "Initial PM reactions: 1937\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6531220000001667\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['FTHFLi', 'TMDK1m'], inactive_NC:['VD3', 'UMPK7', 'NTD5m', 'PVD3', '7DHCHSTEROLtr']\n", + "Zero-expression evidence for reaction...\n", + "1937\n", + "1937\n", + "check_model_function done ....\n", + "Len P: 1097\n", + "num_removed 489\n", + "Len P AFTER 1096\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 489 (69 core, 420 non-core); Num. remaining: 1096\n", + "Reaction no. 125\n", + "Attempting to remove reaction: PROt4_2_r ...\n", + "Initial PM reactions: 1937\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.523490000000038\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['SUCOAS1m'], inactive_NC:['UMPK', 'PROt4_2_r']\n", + "Zero-expression evidence for reaction...\n", + "1937\n", + "1937\n", + "check_model_function done ....\n", + "Len P: 1096\n", + "num_removed 489\n", + "Len P AFTER 1095\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 489 (69 core, 420 non-core); Num. remaining: 1095\n", + "Reaction no. 126\n", + "Attempting to remove reaction: SUCCt4_3 ...\n", + "Initial PM reactions: 1937\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7228750000001583\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['SUCCt4_3', 'SUCCtm', 'EX_succ_e']\n", + "Zero-expression evidence for reaction...\n", + "1937\n", + "1937\n", + "check_model_function done ....\n", + "PM reactions (before): 1937\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1934\n", + "Num. removed: 492 (69 core, 423 non-core); Num. remaining: 1092\n", + "Reaction no. 127\n", + "Attempting to remove reaction: CAt7r ...\n", + "Initial PM reactions: 1934\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9511099999999715\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['NDPK3', 'LEUtec', 'RAI3', 'COAtim'], inactive_NC:['CAt7r']\n", + "Zero-expression evidence for reaction...\n", + "1934\n", + "1934\n", + "check_model_function done ....\n", + "Len P: 1092\n", + "num_removed 492\n", + "Len P AFTER 1091\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 492 (69 core, 423 non-core); Num. remaining: 1091\n", + "Reaction no. 128\n", + "Attempting to remove reaction: AACTOOR ...\n", + "Initial PM reactions: 1934\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9812580000000253\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['ALAtN1', 'NDPK3'], inactive_NC:['GLYATm', 'AOBUTDsm', 'AACTtm', 'AACTOOR']\n", + "Zero-expression evidence for reaction...\n", + "1934\n", + "1934\n", + "check_model_function done ....\n", + "Len P: 1091\n", + "num_removed 492\n", + "Len P AFTER 1090\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 492 (69 core, 423 non-core); Num. remaining: 1090\n", + "Reaction no. 129\n", + "Attempting to remove reaction: FATP7t ...\n", + "Initial PM reactions: 1934\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.941908999999896\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['COAtim'], inactive_NC:['FATP7t', 'CRVNCtr']\n", + "Zero-expression evidence for reaction...\n", + "1934\n", + "1934\n", + "check_model_function done ....\n", + "Len P: 1090\n", + "num_removed 492\n", + "Len P AFTER 1089\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 492 (69 core, 423 non-core); Num. remaining: 1089\n", + "Reaction no. 130\n", + "Attempting to remove reaction: FATP4t ...\n", + "Initial PM reactions: 1934\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.926099000000022\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['COAtim'], inactive_NC:['FATP4t', 'ARACHt']\n", + "Zero-expression evidence for reaction...\n", + "1934\n", + "1934\n", + "check_model_function done ....\n", + "Len P: 1089\n", + "num_removed 492\n", + "Len P AFTER 1088\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 492 (69 core, 423 non-core); Num. remaining: 1088\n", + "Reaction no. 131\n", + "Attempting to remove reaction: FATP8t ...\n", + "Initial PM reactions: 1934\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.913187999999991\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['COAtim', 'FACOAL1822', 'FACOAL224'], inactive_NC:['FATP8t', 'SO4t4_3', 'GHMT2r', 'EX_lneldc_e', 'FATP6t', 'LNELDCt', 'LGNCt', 'EX_adrn_e']\n", + "Zero-expression evidence for reaction...\n", + "1934\n", + "1934\n", + "check_model_function done ....\n", + "Len P: 1088\n", + "num_removed 492\n", + "Len P AFTER 1087\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 492 (69 core, 423 non-core); Num. remaining: 1087\n", + "Reaction no. 132\n", + "Attempting to remove reaction: FATP6t ...\n", + "Initial PM reactions: 1934\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.697161000000051\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['FACOAL224'], inactive_NC:['FATP6t', 'EX_adrn_e']\n", + "Zero-expression evidence for reaction...\n", + "1934\n", + "1934\n", + "check_model_function done ....\n", + "Len P: 1087\n", + "num_removed 492\n", + "Len P AFTER 1086\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 492 (69 core, 423 non-core); Num. remaining: 1086\n", + "Reaction no. 133\n", + "Attempting to remove reaction: FATP9t ...\n", + "Initial PM reactions: 1934\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.644645999999966\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['NKCCt', 'TPI', 'FACOAL241'], inactive_NC:['EX_nrvnc_e', 'FATP9t', 'ARTFR45']\n", + "Zero-expression evidence for reaction...\n", + "1934\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1934\n", + "check_model_function done ....\n", + "Len P: 1086\n", + "num_removed 492\n", + "Len P AFTER 1085\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 492 (69 core, 423 non-core); Num. remaining: 1085\n", + "Reaction no. 134\n", + "Attempting to remove reaction: ASCBt4 ...\n", + "Initial PM reactions: 1934\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6313940000000002\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['NKCCt', 'DHAAt1r', 'COAtim'], inactive_NC:['ASCBt4', 'FE3R2e', 'EX_fe3_e', 'EX_fe2_e']\n", + "Zero-expression evidence for reaction...\n", + "1934\n", + "1934\n", + "check_model_function done ....\n", + "Len P: 1085\n", + "num_removed 492\n", + "Len P AFTER 1084\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 492 (69 core, 423 non-core); Num. remaining: 1084\n", + "Reaction no. 135\n", + "Attempting to remove reaction: FATP5t ...\n", + "Initial PM reactions: 1934\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.950888999999961\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['FACOAL204_copy2', 'MAN6PI', 'PGS'], inactive_NC:['EX_prostgd2_e', 'PROSTGD2t', 'EX_arachd_e', 'MALtm', 'THRGLNexR', 'FATP5t', 'PGDI']\n", + "Zero-expression evidence for reaction...\n", + "1934\n", + "1934\n", + "check_model_function done ....\n", + "Len P: 1084\n", + "num_removed 492\n", + "Len P AFTER 1083\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 492 (69 core, 423 non-core); Num. remaining: 1083\n", + "Reaction no. 136\n", + "Attempting to remove reaction: INSTt4 ...\n", + "Initial PM reactions: 1934\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9616189999999278\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['INSTt4', 'INSTt4_2']\n", + "Zero-expression evidence for reaction...\n", + "1934\n", + "1934\n", + "check_model_function done ....\n", + "PM reactions (before): 1934\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1932\n", + "Num. removed: 494 (69 core, 425 non-core); Num. remaining: 1081\n", + "Reaction no. 137\n", + "Attempting to remove reaction: CYTK1n ...\n", + "Initial PM reactions: 1932\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.961270999999897\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['CHOLtu'], inactive_NC:['CYTK13', 'CYTK1n']\n", + "Zero-expression evidence for reaction...\n", + "1932\n", + "1932\n", + "check_model_function done ....\n", + "Len P: 1081\n", + "num_removed 494\n", + "Len P AFTER 1080\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 494 (69 core, 425 non-core); Num. remaining: 1080\n", + "Reaction no. 138\n", + "Attempting to remove reaction: GLYAMDTRc ...\n", + "Initial PM reactions: 1932\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9738669999999274\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CREATt4_2_r', 'ASPTAm'], inactive_NC:['GACMTRc', 'EX_creat_e', 'PROt4_2_r', 'GLYAMDTRc']\n", + "Zero-expression evidence for reaction...\n", + "1932\n", + "1932\n", + "check_model_function done ....\n", + "Len P: 1080\n", + "num_removed 494\n", + "Len P AFTER 1079\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 494 (69 core, 425 non-core); Num. remaining: 1079\n", + "Reaction no. 139\n", + "Attempting to remove reaction: CHTNASEe ...\n", + "Initial PM reactions: 1932\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9686850000000504\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['MAN6PI'], inactive_NC:['CHTNASEe', 'EX_retfa_e', 'EX_chtn_e', 'EX_acgam_e', 'It']\n", + "Zero-expression evidence for reaction...\n", + "1932\n", + "1932\n", + "check_model_function done ....\n", + "PM reactions (before): 1932\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1926\n", + "Num. removed: 500 (70 core, 430 non-core); Num. remaining: 1075\n", + "Reaction no. 140\n", + "Attempting to remove reaction: ESTRONESt2 ...\n", + "Initial PM reactions: 1926\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 18 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6517790000000332\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 19 , inactive_C: ['UGT1A6r', 'UGT1A1r', 'HSD17B8r', 'HSD17B7r', 'ESTRADIOLGLCt2'], inactive_NC:['ESTRONEGLCt', 'P4501B1r', 'ESTRONEGLCtr', 'EX_estradiolglc_e', 'HESTRATRIOLtr', 'EX_estroneglc_e', 'EX_hestratriol_e', 'ESTRADIOLGLCtr', 'ESTRONESt2', 'EX_hco3_e', 'L_LACt4r', 'ESTRONEtr', 'HESTRATRIOLte', 'EX_estrones_e']\n", + "Zero-expression evidence for reaction...\n", + "1926\n", + "1926\n", + "check_model_function done ....\n", + "Len P: 1075\n", + "num_removed 500\n", + "Len P AFTER 1074\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 500 (70 core, 430 non-core); Num. remaining: 1074\n", + "Reaction no. 141\n", + "Attempting to remove reaction: ACP1_FMN ...\n", + "Initial PM reactions: 1926\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5848419999999805\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['RBFK', 'L_LACt2r', 'MTHFD2m', 'FACOAL1822', 'COAtim', 'RDH1a'], inactive_NC:['ACP1_FMN', 'HIStN1', 'LNELDCt', 'EX_lneldc_e']\n", + "Zero-expression evidence for reaction...\n", + "1926\n", + "1926\n", + "check_model_function done ....\n", + "Len P: 1074\n", + "num_removed 500\n", + "Len P AFTER 1073\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 500 (70 core, 430 non-core); Num. remaining: 1073\n", + "Reaction no. 142\n", + "Attempting to remove reaction: SERHL ...\n", + "Initial PM reactions: 1926\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8865829999999733\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['CHOLtu', 'MTHFD2m'], inactive_NC:['GHMT2r', 'SERHL']\n", + "Zero-expression evidence for reaction...\n", + "1926\n", + "1926\n", + "check_model_function done ....\n", + "Len P: 1073\n", + "num_removed 500\n", + "Len P AFTER 1072\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 500 (70 core, 430 non-core); Num. remaining: 1072\n", + "Reaction no. 143\n", + "Attempting to remove reaction: UMPK ...\n", + "Initial PM reactions: 1926\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.947898000000123\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['COAtim'], inactive_NC:['UMPK']\n", + "Zero-expression evidence for reaction...\n", + "1926\n", + "1926\n", + "check_model_function done ....\n", + "Len P: 1072\n", + "num_removed 500\n", + "Len P AFTER 1071\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 500 (70 core, 430 non-core); Num. remaining: 1071\n", + "Reaction no. 144\n", + "Attempting to remove reaction: TSULt4_3 ...\n", + "Initial PM reactions: 1926\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9194720000000416\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CYANSTm'], inactive_NC:['TSULt4_3', 'FUMTSULtm', 'EX_tsul_e', 'CYANtm', 'TCYNTtm']\n", + "Zero-expression evidence for reaction...\n", + "1926\n", + "1926\n", + "check_model_function done ....\n", + "PM reactions (before): 1926\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1920\n", + "Num. removed: 506 (71 core, 435 non-core); Num. remaining: 1066\n", + "Reaction no. 145\n", + "Attempting to remove reaction: 5ADTSTSTERONESULT ...\n", + "Initial PM reactions: 1920\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 13 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.887098000000151\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 14 , inactive_C: ['PGM', 'TPI', 'ENO', 'CHOLtu', 'SERtN1', 'FACOAL1822'], inactive_NC:['ALAt2r', 'EX_lneldc_e', 'LNELDCt', 'EX_5adtststerones_e', '5ADTSTSTERONESte', 'PROt4_2_r', 'PROSTGE2t2', '5ADTSTSTERONESULT']\n", + "Zero-expression evidence for reaction...\n", + "1920\n", + "1920\n", + "check_model_function done ....\n", + "Len P: 1066\n", + "num_removed 506\n", + "Len P AFTER 1065\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 506 (71 core, 435 non-core); Num. remaining: 1065\n", + "Reaction no. 146\n", + "Attempting to remove reaction: DHEASULT ...\n", + "Initial PM reactions: 1920\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.869271000000026\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['PIt8', 'STS1', 'LDH_Lm'], inactive_NC:['DHEASULT', 'CYTK13', 'PROSTGE2t', 'HIStN1', 'NCNt']\n", + "Zero-expression evidence for reaction...\n", + "1920\n", + "1920\n", + "check_model_function done ....\n", + "Len P: 1065\n", + "num_removed 506\n", + "Len P AFTER 1064\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 506 (71 core, 435 non-core); Num. remaining: 1064\n", + "Reaction no. 147\n", + "Attempting to remove reaction: BPNT2 ...\n", + "Initial PM reactions: 1920\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.835890000000063\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['BPNT2']\n", + "Zero-expression evidence for reaction...\n", + "1920\n", + "1920\n", + "check_model_function done ....\n", + "PM reactions (before): 1920\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1919\n", + "Num. removed: 507 (71 core, 436 non-core); Num. remaining: 1063\n", + "Reaction no. 148\n", + "Attempting to remove reaction: UMPKn ...\n", + "Initial PM reactions: 1919\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9561570000000756\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['NDPK7n', 'MTHFD2m', 'COAtim'], inactive_NC:['UMPK6n', 'ADEt', 'UMPKn', 'DOPAt4_2_r', 'CYTK1', 'EX_ade_e']\n", + "Zero-expression evidence for reaction...\n", + "1919\n", + "1919\n", + "check_model_function done ....\n", + "Len P: 1063\n", + "num_removed 507\n", + "Len P AFTER 1062\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 507 (71 core, 436 non-core); Num. remaining: 1062\n", + "Reaction no. 149\n", + "Attempting to remove reaction: NRPPHRt4_2_r ...\n", + "Initial PM reactions: 1919\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6241820000000189\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['NRPPHRVESSEC', 'NRPPHRt4_2_r', 'HIStN1']\n", + "Zero-expression evidence for reaction...\n", + "1919\n", + "1919\n", + "check_model_function done ....\n", + "PM reactions (before): 1919\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1916\n", + "Num. removed: 510 (71 core, 439 non-core); Num. remaining: 1059\n", + "Reaction no. 150\n", + "Attempting to remove reaction: RDH1 ...\n", + "Initial PM reactions: 1916\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 15 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5836259999998674\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 16 , inactive_C: ['CHOLtu', 'PUNP1', 'MTHFD2m', 'URIt', 'LEUtec'], inactive_NC:['EX_pi_e', 'VD3', 'CYTK13', 'RETI3', 'RDH4', 'PROt4_2_r', 'RADH4', 'DOPAt4_2_r', 'RDH1', 'PVD3', '7DHCHSTEROLtr']\n", + "Zero-expression evidence for reaction...\n", + "1916\n", + "1916\n", + "check_model_function done ....\n", + "Len P: 1059\n", + "num_removed 510\n", + "Len P AFTER 1058\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 510 (71 core, 439 non-core); Num. remaining: 1058\n", + "Reaction no. 151\n", + "Attempting to remove reaction: RDH3 ...\n", + "Initial PM reactions: 1916\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8248109999999542\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['DCMPDA', 'RDH3a', 'CHOLtu', 'URIt', 'COAtim'], inactive_NC:['EX_pi_e', 'RDH3']\n", + "Zero-expression evidence for reaction...\n", + "1916\n", + "1916\n", + "check_model_function done ....\n", + "Len P: 1058\n", + "num_removed 510\n", + "Len P AFTER 1057\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 510 (71 core, 439 non-core); Num. remaining: 1057\n", + "Reaction no. 152\n", + "Attempting to remove reaction: RDH4 ...\n", + "Initial PM reactions: 1916\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8704649999999674\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['ASNtN1'], inactive_NC:['RDH4', 'RADH4', 'RETI3']\n", + "Zero-expression evidence for reaction...\n", + "1916\n", + "1916\n", + "check_model_function done ....\n", + "PM reactions (before): 1916\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1912\n", + "Num. removed: 514 (72 core, 442 non-core); Num. remaining: 1054\n", + "Reaction no. 153\n", + "Attempting to remove reaction: DOPAt4_2_r ...\n", + "Initial PM reactions: 1912\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.87480800000003\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['NDPK3', 'FACOAL1822', 'ASPTAm'], inactive_NC:['EX_lneldc_e', 'THRGLYexR', 'LNELDCt', 'DOPAt4_2_r', 'RDH1']\n", + "Zero-expression evidence for reaction...\n", + "1912\n", + "1912\n", + "check_model_function done ....\n", + "Len P: 1054\n", + "num_removed 514\n", + "Len P AFTER 1053\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 514 (72 core, 442 non-core); Num. remaining: 1053\n", + "Reaction no. 154\n", + "Attempting to remove reaction: FRUt4 ...\n", + "Initial PM reactions: 1912\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9715869999999995\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['ALAtN1'], inactive_NC:['FRUt4', 'SUCRe', 'EX_sucr_e']\n", + "Zero-expression evidence for reaction...\n", + "1912\n", + "1912\n", + "check_model_function done ....\n", + "PM reactions (before): 1912\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1908\n", + "Num. removed: 518 (73 core, 445 non-core); Num. remaining: 1050\n", + "Reaction no. 155\n", + "Attempting to remove reaction: SRTNt6_2_r ...\n", + "Initial PM reactions: 1908\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.896633999999949\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['ALCD1', 'ASPTAm'], inactive_NC:['5HLTDL', 'SRTNt6_2_r', 'EX_srtn_e']\n", + "Zero-expression evidence for reaction...\n", + "1908\n", + "1908\n", + "check_model_function done ....\n", + "Len P: 1050\n", + "num_removed 518\n", + "Len P AFTER 1049\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 518 (73 core, 445 non-core); Num. remaining: 1049\n", + "Reaction no. 156\n", + "Attempting to remove reaction: NADNe ...\n", + "Initial PM reactions: 1908\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8478110000000925\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['EX_nad_e', 'NADNe', 'ADPRIBt']\n", + "Zero-expression evidence for reaction...\n", + "1908\n", + "1908\n", + "check_model_function done ....\n", + "PM reactions (before): 1908\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1905\n", + "Num. removed: 521 (73 core, 448 non-core); Num. remaining: 1047\n", + "Reaction no. 157\n", + "Attempting to remove reaction: NADPNe ...\n", + "Initial PM reactions: 1905\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.913724000000002\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['FUM', 'NDPK5m'], inactive_NC:['CYTK13', 'EX_nadp_e', 'EX_adprbp_e', 'EX_ncam_e', 'NADPNe']\n", + "Zero-expression evidence for reaction...\n", + "1905\n", + "1905\n", + "check_model_function done ....\n", + "Len P: 1047\n", + "num_removed 521\n", + "Len P AFTER 1046\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 521 (73 core, 448 non-core); Num. remaining: 1046\n", + "Reaction no. 158\n", + "Attempting to remove reaction: LPS3e ...\n", + "Initial PM reactions: 1905\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.919403999999986\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['LPSe'], inactive_NC:['EX_Rtotal_e', 'EX_glyc_e', 'EX_tag_hs_e', 'LPS3e', 'EX_Rtotal3_e', 'LPS2e']\n", + "Zero-expression evidence for reaction...\n", + "1905\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1905\n", + "check_model_function done ....\n", + "PM reactions (before): 1905\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1898\n", + "Num. removed: 528 (74 core, 454 non-core); Num. remaining: 1040\n", + "Reaction no. 159\n", + "Attempting to remove reaction: LPS4e ...\n", + "Initial PM reactions: 1898\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9253980000000865\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['EX_pglyc_hs_e', 'EX_1glyc_hs_e', 'LPS4e']\n", + "Zero-expression evidence for reaction...\n", + "1898\n", + "1898\n", + "check_model_function done ....\n", + "PM reactions (before): 1898\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1895\n", + "Num. removed: 531 (74 core, 457 non-core); Num. remaining: 1037\n", + "Reaction no. 160\n", + "Attempting to remove reaction: PAFHe ...\n", + "Initial PM reactions: 1895\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9391259999999875\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['FACOAL184'], inactive_NC:['EX_ak2lgchol_hs_e', 'PAFHe', 'EX_strdnc_e', 'EX_paf_hs_e', 'STRDNCt']\n", + "Zero-expression evidence for reaction...\n", + "1895\n", + "1895\n", + "check_model_function done ....\n", + "PM reactions (before): 1895\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1889\n", + "Num. removed: 537 (75 core, 462 non-core); Num. remaining: 1032\n", + "Reaction no. 161\n", + "Attempting to remove reaction: P5CRx ...\n", + "Initial PM reactions: 1889\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8430539999999382\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['NDPK4m', 'L_LACt2r', 'CHOLtu', 'MTHFD2m', 'CYStec'], inactive_NC:['PROt2r', 'P5CRx']\n", + "Zero-expression evidence for reaction...\n", + "1889\n", + "1889\n", + "check_model_function done ....\n", + "Len P: 1032\n", + "num_removed 537\n", + "Len P AFTER 1031\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 537 (75 core, 462 non-core); Num. remaining: 1031\n", + "Reaction no. 162\n", + "Attempting to remove reaction: PRO1x ...\n", + "Initial PM reactions: 1889\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9556739999998172\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['PPM', 'NDPK3', 'FTHFLi', 'RDH1a'], inactive_NC:['PRO1x', 'MALtm']\n", + "Zero-expression evidence for reaction...\n", + "1889\n", + "1889\n", + "check_model_function done ....\n", + "Len P: 1031\n", + "num_removed 537\n", + "Len P AFTER 1030\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 537 (75 core, 462 non-core); Num. remaining: 1030\n", + "Reaction no. 163\n", + "Attempting to remove reaction: GNMT ...\n", + "Initial PM reactions: 1889\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.705543999999918\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['GNMT']\n", + "Zero-expression evidence for reaction...\n", + "1889\n", + "1889\n", + "check_model_function done ....\n", + "PM reactions (before): 1889\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1888\n", + "Num. removed: 538 (75 core, 463 non-core); Num. remaining: 1029\n", + "Reaction no. 164\n", + "Attempting to remove reaction: GACMTRc ...\n", + "Initial PM reactions: 1888\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9475800000000163\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['CREATt4_2_r', 'FACOAL1822'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'EX_lneldc_e', 'LNELDCt', 'GACMTRc']\n", + "Zero-expression evidence for reaction...\n", + "1888\n", + "1888\n", + "check_model_function done ....\n", + "Len P: 1029\n", + "num_removed 538\n", + "Len P AFTER 1028\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 538 (75 core, 463 non-core); Num. remaining: 1028\n", + "Reaction no. 165\n", + "Attempting to remove reaction: ETHP ...\n", + "Initial PM reactions: 1888\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8904399999998986\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['L_LACtm'], inactive_NC:['ETHP']\n", + "Zero-expression evidence for reaction...\n", + "1888\n", + "1888\n", + "check_model_function done ....\n", + "Len P: 1028\n", + "num_removed 538\n", + "Len P AFTER 1027\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 538 (75 core, 463 non-core); Num. remaining: 1027\n", + "Reaction no. 166\n", + "Attempting to remove reaction: SO4t4_3 ...\n", + "Initial PM reactions: 1888\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5710270000001856\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['DCMPDA', 'CHOLtu', 'SERtN1', 'URIt', 'LEUtec'], inactive_NC:['RDH1', 'SO4t4_3']\n", + "Zero-expression evidence for reaction...\n", + "1888\n", + "1888\n", + "check_model_function done ....\n", + "Len P: 1027\n", + "num_removed 538\n", + "Len P AFTER 1026\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 538 (75 core, 463 non-core); Num. remaining: 1026\n", + "Reaction no. 167\n", + "Attempting to remove reaction: P4504F123r ...\n", + "Initial PM reactions: 1888\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5437839999999596\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: [], inactive_NC:['EX_pi_e', 'EBASTINEte', 'EX_ebastineoh_e', 'P4504F123r', 'EBASTINEtr', 'EBASTINEOHtr', 'EBASTINEOHte', 'EX_ebastine_e']\n", + "Zero-expression evidence for reaction...\n", + "1888\n", + "1888\n", + "check_model_function done ....\n", + "Len P: 1026\n", + "num_removed 538\n", + "Len P AFTER 1025\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 538 (75 core, 463 non-core); Num. remaining: 1025\n", + "Reaction no. 168\n", + "Attempting to remove reaction: P45039A1r ...\n", + "Initial PM reactions: 1888\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5825019999999768\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['XOLTRI24te', 'XOLTRI24tc', 'P45039A1r', 'P45046A1r', 'EX_xoltri24_e']\n", + "Zero-expression evidence for reaction...\n", + "1888\n", + "1888\n", + "check_model_function done ....\n", + "PM reactions (before): 1888\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1883\n", + "Num. removed: 543 (75 core, 468 non-core); Num. remaining: 1020\n", + "Reaction no. 169\n", + "Attempting to remove reaction: SGPL12r ...\n", + "Initial PM reactions: 1883\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5881799999999657\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['CHOLtu', 'ASAH1'], inactive_NC:['SPHMDAc', 'DM_ethamp_r', 'HDCAter', 'SPHINGStl', 'SPHMYLNtl', 'SMPD4', 'SMPD3l', 'Rtotaltl', 'CHOLPtl', 'SGPL12r']\n", + "Zero-expression evidence for reaction...\n", + "1883\n", + "1883\n", + "check_model_function done ....\n", + "PM reactions (before): 1883\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1871\n", + "Num. removed: 555 (77 core, 478 non-core); Num. remaining: 1010\n", + "Reaction no. 170\n", + "Attempting to remove reaction: HSD3B2r ...\n", + "Initial PM reactions: 1871\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5064640000000509\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['DCMPDA', 'RDH1a', 'MTHFD2m'], inactive_NC:['HSD3B2r']\n", + "Zero-expression evidence for reaction...\n", + "1871\n", + "1871\n", + "check_model_function done ....\n", + "Len P: 1010\n", + "num_removed 555\n", + "Len P AFTER 1009\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 555 (77 core, 478 non-core); Num. remaining: 1009\n", + "Reaction no. 171\n", + "Attempting to remove reaction: HSD3B3r ...\n", + "Initial PM reactions: 1871\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5330329999999321\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['MTHFD2m', 'NDPK3', 'ACACt2', 'LDH_Lm'], inactive_NC:['CYTK8', 'EX_cit_e', 'CYTK13', 'CITt4_2', 'HSD3B3r', 'EX_acac_e', 'PROt4_2_r']\n", + "Zero-expression evidence for reaction...\n", + "1871\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1871\n", + "check_model_function done ....\n", + "Len P: 1009\n", + "num_removed 555\n", + "Len P AFTER 1008\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 555 (77 core, 478 non-core); Num. remaining: 1008\n", + "Reaction no. 172\n", + "Attempting to remove reaction: PCHOLPr_hs ...\n", + "Initial PM reactions: 1871\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 21 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5846829999998135\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 22 , inactive_C: ['DCMPDA', 'FACOAL161', 'PSSA2_hs', 'PETHCT', 'PETOHMr_hs', 'LDH_Lm', 'SMS', 'PGPPT', 'URIt'], inactive_NC:['biomass_mac', 'PE_HSter', 'AMETr', 'CHOLtr', 'CEPTE', 'EX_pe_hs_e', 'PA_HSter', 'PCHOLPr_hs', 'PGPP_hs', 'PSFLIP', 'PEFLIP', 'EX_ps_hs_e', 'AHCYStr']\n", + "Zero-expression evidence for reaction...\n", + "1871\n", + "1871\n", + "check_model_function done ....\n", + "Len P: 1008\n", + "num_removed 555\n", + "Len P AFTER 1007\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 555 (77 core, 478 non-core); Num. remaining: 1007\n", + "Reaction no. 173\n", + "Attempting to remove reaction: 5HLTDL ...\n", + "Initial PM reactions: 1871\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.515137999999979\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['FACOAL1822', 'NDPK4m'], inactive_NC:['5HLTDL', 'EX_lneldc_e', 'EX_srtn_e', 'LNELDCt', 'DOPAt4_2_r', 'SRTNt6_2_r']\n", + "Zero-expression evidence for reaction...\n", + "1871\n", + "1871\n", + "check_model_function done ....\n", + "PM reactions (before): 1871\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1863\n", + "Num. removed: 563 (79 core, 484 non-core); Num. remaining: 1003\n", + "Reaction no. 174\n", + "Attempting to remove reaction: TREHe ...\n", + "Initial PM reactions: 1863\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.490929000000051\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['EX_tre_e', 'TREHe']\n", + "Zero-expression evidence for reaction...\n", + "1863\n", + "1863\n", + "check_model_function done ....\n", + "PM reactions (before): 1863\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1861\n", + "Num. removed: 565 (79 core, 486 non-core); Num. remaining: 1001\n", + "Reaction no. 175\n", + "Attempting to remove reaction: O16G1e ...\n", + "Initial PM reactions: 1861\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5503510000000915\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['AMY2e'], inactive_NC:['O16G1e', 'EX_glygn2_e', 'EX_Tyr_ggn_e', 'GAMYe']\n", + "Zero-expression evidence for reaction...\n", + "1861\n", + "1861\n", + "check_model_function done ....\n", + "PM reactions (before): 1861\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1856\n", + "Num. removed: 570 (80 core, 490 non-core); Num. remaining: 997\n", + "Reaction no. 176\n", + "Attempting to remove reaction: MOGAT ...\n", + "Initial PM reactions: 1856\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4005429999999706\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['MOGAT']\n", + "Zero-expression evidence for reaction...\n", + "1856\n", + "1856\n", + "check_model_function done ....\n", + "PM reactions (before): 1856\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1855\n", + "Num. removed: 571 (80 core, 491 non-core); Num. remaining: 996\n", + "Reaction no. 177\n", + "Attempting to remove reaction: IDHPOXOX2b ...\n", + "Initial PM reactions: 1855\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 13 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5128159999999298\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 14 , inactive_C: ['TRIODTHYSULT', 'TPI'], inactive_NC:['THYOXt', 'IDHPOXOX3', 'CYTK13', 'IDHPOXOXb', 'THYPX', 'EX_triodthysuf_e', 'TRIODTHYSUFt', 'IDHPOXOX2b', 'EX_thyox__L_e', 'IDHPOXOX4', 'PROSTGE2t2', 'EX_i_e']\n", + "Zero-expression evidence for reaction...\n", + "1855\n", + "1855\n", + "check_model_function done ....\n", + "PM reactions (before): 1855\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1841\n", + "Num. removed: 585 (82 core, 503 non-core); Num. remaining: 986\n", + "Reaction no. 178\n", + "Attempting to remove reaction: PHYCBOXL ...\n", + "Initial PM reactions: 1841\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.545381000000134\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['PEAMNO', 'NDPK3', 'ALDD19xr', 'ALDD19x_P'], inactive_NC:['PACCOAL', 'EX_pheacgln_e', 'PHEACGLNt', 'PHACCOAGLNAC', 'HMGCOAtm', 'PHYCBOXL']\n", + "Zero-expression evidence for reaction...\n", + "1841\n", + "1841\n", + "check_model_function done ....\n", + "Len P: 986\n", + "num_removed 585\n", + "Len P AFTER 985\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 585 (82 core, 503 non-core); Num. remaining: 985\n", + "Reaction no. 179\n", + "Attempting to remove reaction: UGT1A9r ...\n", + "Initial PM reactions: 1841\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5015740000001188\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['2HBO', 'SERtN1', 'LEUtec', 'RDH1a', '2HBt2'], inactive_NC:['5ADTSTSTERONEtr', '5ADTSTSTERONEGLCtr', '5ADTSTSTERONEGLCte', 'PROt4_2_r', 'EX_2hb_e', 'EX_5adtststeroneglc_e', 'UGT1A9r']\n", + "Zero-expression evidence for reaction...\n", + "1841\n", + "1841\n", + "check_model_function done ....\n", + "Len P: 985\n", + "num_removed 585\n", + "Len P AFTER 984\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 585 (82 core, 503 non-core); Num. remaining: 984\n", + "Reaction no. 180\n", + "Attempting to remove reaction: P4502C18 ...\n", + "Initial PM reactions: 1841\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.552005999999892\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['NKCCt', 'ACACt2'], inactive_NC:['EX_dmantipyrine_e', 'CYTK2', 'EX_antipyrene_e', 'ANTIPYRENEte', 'P4502C18', 'DMANTIPYRINEte', 'EX_acac_e']\n", + "Zero-expression evidence for reaction...\n", + "1841\n", + "1841\n", + "check_model_function done ....\n", + "PM reactions (before): 1841\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1832\n", + "Num. removed: 594 (84 core, 510 non-core); Num. remaining: 977\n", + "Reaction no. 181\n", + "Attempting to remove reaction: NAt5 ...\n", + "Initial PM reactions: 1832\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5692699999999604\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['NAt5']\n", + "Zero-expression evidence for reaction...\n", + "1832\n", + "1832\n", + "check_model_function done ....\n", + "PM reactions (before): 1832\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1831\n", + "Num. removed: 595 (84 core, 511 non-core); Num. remaining: 976\n", + "Reaction no. 182\n", + "Attempting to remove reaction: MCDm ...\n", + "Initial PM reactions: 1831\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4741460000000188\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: [], inactive_NC:['CYTK8', 'ACCOACrm', 'MCDm', 'EX_glc__D_e']\n", + "Zero-expression evidence for reaction...\n", + "1831\n", + "1831\n", + "check_model_function done ....\n", + "PM reactions (before): 1831\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1827\n", + "Num. removed: 599 (84 core, 515 non-core); Num. remaining: 973\n", + "Reaction no. 183\n", + "Attempting to remove reaction: DURAD2 ...\n", + "Initial PM reactions: 1827\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5677370000000792\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['TMDPP'], inactive_NC:['D_3AIBt', 'DHPM2', 'BUP2', 'DURAD2', 'EX_3aib__D_e']\n", + "Zero-expression evidence for reaction...\n", + "1827\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1827\n", + "check_model_function done ....\n", + "PM reactions (before): 1827\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1821\n", + "Num. removed: 605 (85 core, 520 non-core); Num. remaining: 968\n", + "Reaction no. 184\n", + "Attempting to remove reaction: P5CR ...\n", + "Initial PM reactions: 1821\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5322380000000067\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['P5CR', 'RDH1']\n", + "Zero-expression evidence for reaction...\n", + "1821\n", + "1821\n", + "check_model_function done ....\n", + "PM reactions (before): 1821\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1819\n", + "Num. removed: 607 (85 core, 522 non-core); Num. remaining: 967\n", + "Reaction no. 185\n", + "Attempting to remove reaction: PPAP ...\n", + "Initial PM reactions: 1819\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4167070000000876\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['MDHm', 'PUNP5', 'URIt'], inactive_NC:['L_LACt4r', 'PPAP', 'CYTK10']\n", + "Zero-expression evidence for reaction...\n", + "1819\n", + "1819\n", + "check_model_function done ....\n", + "Len P: 967\n", + "num_removed 607\n", + "Len P AFTER 966\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 607 (85 core, 522 non-core); Num. remaining: 966\n", + "Reaction no. 186\n", + "Attempting to remove reaction: MCD ...\n", + "Initial PM reactions: 1819\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4726670000000013\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['PUNP5', 'FACOAL224', 'MTHFD2m', 'COAtim', 'LEUtec'], inactive_NC:['MCD', 'CYTK10', 'FATP6t', 'EX_adrn_e']\n", + "Zero-expression evidence for reaction...\n", + "1819\n", + "1819\n", + "check_model_function done ....\n", + "Len P: 966\n", + "num_removed 607\n", + "Len P AFTER 965\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 607 (85 core, 522 non-core); Num. remaining: 965\n", + "Reaction no. 187\n", + "Attempting to remove reaction: TRDR ...\n", + "Initial PM reactions: 1819\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 51 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7520010000000639\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 52 , inactive_C: ['FTHFLi', 'NKCC2t', 'DUTPDPn', 'PETOHMr_hs', 'SMS', 'NDPK3', 'PGPPT', 'CYStec', 'NDPK7', 'RNDR4', 'RNDR3', 'PSSA2_hs', 'PPM', 'FACOAL161', 'TMDS', 'PETHCT', 'RNDR2', 'NDPK6n', 'RNDR1'], inactive_NC:['DNDPt56m', 'CEPTE', 'PA_HSter', 'DM_dctp_n', 'DM_dctp_m', 'AHCYStr', 'AMETr', 'CHOLtr', 'DUDPtn', 'DNDPt55m', 'PCHOLPr_hs', 'PGPP_hs', 'DM_datp_m', 'PSFLIP', 'DM_dgtp_n', 'DGTPtn', 'DUMPtn', 'DNDPt52m', 'TRDR', 'DCTPtn', 'PEFLIP', 'EX_ps_hs_e', 'NDP8', 'biomass_mac', 'DNDPt53m', 'DM_dgtp_m', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt51m', 'DNDPt54m', 'DM_datp_n', 'DATPtn', 'NDP6']\n", + "Zero-expression evidence for reaction...\n", + "1819\n", + "1819\n", + "check_model_function done ....\n", + "Len P: 965\n", + "num_removed 607\n", + "Len P AFTER 964\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 607 (85 core, 522 non-core); Num. remaining: 964\n", + "Reaction no. 188\n", + "Attempting to remove reaction: NORANMT ...\n", + "Initial PM reactions: 1819\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 13 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.457730999999967\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 14 , inactive_C: ['41R1H2MAE12BOOX', 'GLNtN1', 'SALMCOM2', 'SFGTHi', 'MTHFD2m', 'URIt', 'FALDH'], inactive_NC:['NORANMT', 'EX_adrnl_e', 'ADRNLPVESSEC', 'MEPIVESSte', 'MAOX', 'EX_mepi_e', 'CYTK10']\n", + "Zero-expression evidence for reaction...\n", + "1819\n", + "1819\n", + "check_model_function done ....\n", + "Len P: 964\n", + "num_removed 607\n", + "Len P AFTER 963\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 607 (85 core, 522 non-core); Num. remaining: 963\n", + "Reaction no. 189\n", + "Attempting to remove reaction: DURAD ...\n", + "Initial PM reactions: 1819\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4353099999998449\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['DHPM1', 'CYStec', 'PYNP2r'], inactive_NC:['UPPN', 'DURAD', 'CYTK10']\n", + "Zero-expression evidence for reaction...\n", + "1819\n", + "1819\n", + "check_model_function done ....\n", + "Len P: 963\n", + "num_removed 607\n", + "Len P AFTER 962\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 607 (85 core, 522 non-core); Num. remaining: 962\n", + "Reaction no. 190\n", + "Attempting to remove reaction: TYRCBOX ...\n", + "Initial PM reactions: 1819\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 16 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4710509999999886\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 17 , inactive_C: ['2HBO', 'TYROXDAc', 'ASPGLUm', '4HOXPACDOX_NADP', 'TYMSULT', 'COAtim', '2HBt2'], inactive_NC:['EX_pi_e', 'GHMT2r', 'TYRCBOX', 'ADEt', 'EX_tymsf_e', 'EX_ade_e', 'HPACtr', 'EX_2hb_e', 'EX_4hphac_e', 'TYMSFt']\n", + "Zero-expression evidence for reaction...\n", + "1819\n", + "1819\n", + "check_model_function done ....\n", + "Len P: 962\n", + "num_removed 607\n", + "Len P AFTER 961\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 607 (85 core, 522 non-core); Num. remaining: 961\n", + "Reaction no. 191\n", + "Attempting to remove reaction: GLCt4_2 ...\n", + "Initial PM reactions: 1819\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.561786000000211\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['ACACT1r_copy2'], inactive_NC:['EX_akg_e', 'GLCt4_2', 'AKGt4_3']\n", + "Zero-expression evidence for reaction...\n", + "1819\n", + "1819\n", + "check_model_function done ....\n", + "PM reactions (before): 1819\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1815\n", + "Num. removed: 611 (86 core, 525 non-core); Num. remaining: 958\n", + "Reaction no. 192\n", + "Attempting to remove reaction: GLCt4 ...\n", + "Initial PM reactions: 1815\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4505090000002383\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['SERtN1', 'MTHFD2m', 'COAtim'], inactive_NC:['CYTK1', 'GLCt4']\n", + "Zero-expression evidence for reaction...\n", + "1815\n", + "1815\n", + "check_model_function done ....\n", + "Len P: 958\n", + "num_removed 611\n", + "Len P AFTER 957\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 611 (86 core, 525 non-core); Num. remaining: 957\n", + "Reaction no. 193\n", + "Attempting to remove reaction: 3HLYTCL ...\n", + "Initial PM reactions: 1815\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 26 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.607136999999966\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 27 , inactive_C: ['34DHOXPEGOX', '41R1H2MAE12BOOX', 'FALDH', 'SALMCOM2', 'SFGTHi', '41R2A1H12BOOX', 'DOPASULT', 'LEUtec'], inactive_NC:['NRPPHRSULT', 'DOPAVESSEC', 'EX_34dhoxpeg_e', 'EX_dopasf_e', 'MAOX', 'EX_dopa_e', 'DOPABMO', 'EX_adrnl_e', 'DOPASFt', 'ADRNLPVESSEC', 'TYR3MO2', 'NORANMT', '34DHOXPEGt', '3HLYTCL', 'EX_mepi_e', 'MEPIVESSte', 'TYRDOPO', 'NRPPHRSFt', 'EX_nrpphrsf_e']\n", + "Zero-expression evidence for reaction...\n", + "1815\n", + "1815\n", + "check_model_function done ....\n", + "Len P: 957\n", + "num_removed 611\n", + "Len P AFTER 956\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 611 (86 core, 525 non-core); Num. remaining: 956\n", + "Reaction no. 194\n", + "Attempting to remove reaction: BDHm ...\n", + "Initial PM reactions: 1815\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4597890000000007\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['NDPK3', '2HBt2', '2HBO', 'SUCD1m'], inactive_NC:['EX_bhb_e', 'BHBt', 'BDHm', 'EX_2hb_e', 'BHBtm', 'CYTK10']\n", + "Zero-expression evidence for reaction...\n", + "1815\n", + "1815\n", + "check_model_function done ....\n", + "Len P: 956\n", + "num_removed 611\n", + "Len P AFTER 955\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 611 (86 core, 525 non-core); Num. remaining: 955\n", + "Reaction no. 195\n", + "Attempting to remove reaction: VITD3Hm ...\n", + "Initial PM reactions: 1815\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4832320000000436\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['24_25VITD3Hm', 'NDPK3', 'MTHFD2m', 'PDX5POi'], inactive_NC:['24_25DHVITD3tm', '24_25DHVITD3t', 'EX_pydxn_e', 'PYDXNtr', 'EX_2425dhvitd3_e', 'VITD3Hm']\n", + "Zero-expression evidence for reaction...\n", + "1815\n", + "1815\n", + "check_model_function done ....\n", + "Len P: 955\n", + "num_removed 611\n", + "Len P AFTER 954\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 611 (86 core, 525 non-core); Num. remaining: 954\n", + "Reaction no. 196\n", + "Attempting to remove reaction: P45027A1m ...\n", + "Initial PM reactions: 1815\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4649159999999029\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['NDPK3', 'URIt'], inactive_NC:['XOL27OHtm', 'VD3', 'PVD3', 'EX_xoltri27_e', 'XOLTRI27te', 'P45027A1m', 'XOLTRI27tc', 'P4507B12r', '7DHCHSTEROLtr', 'CYTK10']\n", + "Zero-expression evidence for reaction...\n", + "1815\n", + "1815\n", + "check_model_function done ....\n", + "PM reactions (before): 1815\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1803\n", + "Num. removed: 623 (88 core, 535 non-core); Num. remaining: 945\n", + "Reaction no. 197\n", + "Attempting to remove reaction: LEUTA ...\n", + "Initial PM reactions: 1803\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.418315000000348\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['DCMPDA', 'FUM', 'LEUtec'], inactive_NC:['GHMT2r', 'LEUTA', '4MOPt2im']\n", + "Zero-expression evidence for reaction...\n", + "1803\n", + "1803\n", + "check_model_function done ....\n", + "Len P: 945\n", + "num_removed 623\n", + "Len P AFTER 944\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 623 (88 core, 535 non-core); Num. remaining: 944\n", + "Reaction no. 198\n", + "Attempting to remove reaction: CHOLt4 ...\n", + "Initial PM reactions: 1803\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.523399000000154\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['FUM'], inactive_NC:['ACHVESSEC', 'CHAT', 'CHOLt4', 'HMGCOAtm', 'ACHEe']\n", + "Zero-expression evidence for reaction...\n", + "1803\n", + "1803\n", + "check_model_function done ....\n", + "PM reactions (before): 1803\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1797\n", + "Num. removed: 629 (89 core, 540 non-core); Num. remaining: 939\n", + "Reaction no. 199\n", + "Attempting to remove reaction: CEPTC ...\n", + "Initial PM reactions: 1797\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 43 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6119239999998172\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 44 , inactive_C: ['DCMPDA', 'FTHFLi', 'PLA2_2', 'FACOAL161', 'PSSA2_hs', 'PETHCT', 'PETOHMr_hs', 'ASPTAm', 'SMS', 'CHLPCTD', 'PGPPT', 'PCHOLP_hs', 'RDH2a', 'LPASE', 'MTHFD2m', 'RDH1a'], inactive_NC:['EX_retinol_9_cis_e', 'RETH1e', 'CEPTE', 'PA_HSter', 'RETH2e', 'RETFAt2', 'AHCYStr', 'AMETr', 'CHOLtr', 'RETH1', 'RETH2', 'PCHOLPr_hs', 'PGPP_hs', 'PSFLIP', 'RAI2', 'LRAT1', 'RETFAt1', 'LRAT2', 'CEPTC', 'EX_retinol_cis_11_e', 'LRAT', 'PEFLIP', 'EX_ps_hs_e', 'GPDDA1', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'RETI1']\n", + "Zero-expression evidence for reaction...\n", + "1797\n", + "1797\n", + "check_model_function done ....\n", + "Len P: 939\n", + "num_removed 629\n", + "Len P AFTER 938\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 629 (89 core, 540 non-core); Num. remaining: 938\n", + "Reaction no. 200\n", + "Attempting to remove reaction: MLTG1e ...\n", + "Initial PM reactions: 1797\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6277289999998175\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['MLTG1e', 'EX_malttr_e']\n", + "Zero-expression evidence for reaction...\n", + "1797\n", + "1797\n", + "check_model_function done ....\n", + "PM reactions (before): 1797\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1795\n", + "Num. removed: 631 (89 core, 542 non-core); Num. remaining: 936\n", + "Reaction no. 201\n", + "Attempting to remove reaction: O16G2e ...\n", + "Initial PM reactions: 1795\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5422450000000936\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['AMY1e', 'MALT'], inactive_NC:['EX_strch1_e', 'MALTe', 'FUMtm', 'MALTt1r', 'O16G2e']\n", + "Zero-expression evidence for reaction...\n", + "1795\n", + "1795\n", + "check_model_function done ....\n", + "Len P: 936\n", + "num_removed 631\n", + "Len P AFTER 935\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 631 (89 core, 542 non-core); Num. remaining: 935\n", + "Reaction no. 202\n", + "Attempting to remove reaction: MALTe ...\n", + "Initial PM reactions: 1795\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5165200000001278\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['DCMPDA', 'MTHFD', 'PUNP1', 'MTHFD2m', 'MTHFC'], inactive_NC:['MALTe', 'FUMtm', 'CYTK1']\n", + "Zero-expression evidence for reaction...\n", + "1795\n", + "1795\n", + "check_model_function done ....\n", + "Len P: 935\n", + "num_removed 631\n", + "Len P AFTER 934\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 631 (89 core, 542 non-core); Num. remaining: 934\n", + "Reaction no. 203\n", + "Attempting to remove reaction: PPAm ...\n", + "Initial PM reactions: 1795\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 20 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6252989999998135\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 21 , inactive_C: ['BUTt2r', 'ALDD2xm', 'ACOAD1fm', 'BUTt2m', 'DUTPDPm', 'NDPK6'], inactive_NC:['PPAtm', 'DNDPt41m', 'DNDPt40m', 'ACALDtm', 'DNDPt43m', 'DNDPt37m', 'DNDPt38m', 'DNDPt42m', 'PPAm', 'URIDK2m', 'ACSm', 'FACOAL40im', 'EX_but_e', 'ACCOALm', 'DNDPt39m']\n", + "Zero-expression evidence for reaction...\n", + "1795\n", + "1795\n", + "check_model_function done ....\n", + "Len P: 934\n", + "num_removed 631\n", + "Len P AFTER 933\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 631 (89 core, 542 non-core); Num. remaining: 933\n", + "Reaction no. 204\n", + "Attempting to remove reaction: CEPTE ...\n", + "Initial PM reactions: 1795\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.409871999999723\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['PETHCT', '2HBt2', '2HBO', 'PSSA2_hs'], inactive_NC:['EX_hco3_e', 'CEPTE', 'FUMtm', 'EX_2hb_e']\n", + "Zero-expression evidence for reaction...\n", + "1795\n", + "1795\n", + "check_model_function done ....\n", + "Len P: 933\n", + "num_removed 631\n", + "Len P AFTER 932\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 631 (89 core, 542 non-core); Num. remaining: 932\n", + "Reaction no. 205\n", + "Attempting to remove reaction: PROD2 ...\n", + "Initial PM reactions: 1795\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3992749999997613\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['LEUtec', 'ASPGLUm'], inactive_NC:['PROD2', 'FUMtm']\n", + "Zero-expression evidence for reaction...\n", + "1795\n", + "1795\n", + "check_model_function done ....\n", + "Len P: 932\n", + "num_removed 631\n", + "Len P AFTER 931\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 631 (89 core, 542 non-core); Num. remaining: 931\n", + "Reaction no. 206\n", + "Attempting to remove reaction: SAMHISTA ...\n", + "Initial PM reactions: 1795\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6273850000002312\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['DCMPDA', 'MACOXO'], inactive_NC:['HISDC', 'MHISOR', '3MLDAt', 'FUMtm', 'EX_3mlda_e', 'SAMHISTA']\n", + "Zero-expression evidence for reaction...\n", + "1795\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1795\n", + "check_model_function done ....\n", + "PM reactions (before): 1795\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1787\n", + "Num. removed: 639 (91 core, 548 non-core); Num. remaining: 925\n", + "Reaction no. 207\n", + "Attempting to remove reaction: G6PDH1er_copy1 ...\n", + "Initial PM reactions: 1787\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5274139999996805\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['G6PDH2er', 'G6PDH1er_copy1']\n", + "Zero-expression evidence for reaction...\n", + "1787\n", + "1787\n", + "check_model_function done ....\n", + "PM reactions (before): 1787\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1785\n", + "Num. removed: 641 (91 core, 550 non-core); Num. remaining: 923\n", + "Reaction no. 208\n", + "Attempting to remove reaction: HAS2 ...\n", + "Initial PM reactions: 1785\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5082459999998719\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['GLCAASE9ly', 'GLCAASE8ly', 'GLCURtly', 'NACHEX27ly'], inactive_NC:['EX_gln__L_e', 'HAS2', 'HAtly', 'HAS1']\n", + "Zero-expression evidence for reaction...\n", + "1785\n", + "1785\n", + "check_model_function done ....\n", + "Len P: 923\n", + "num_removed 641\n", + "Len P AFTER 922\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 641 (91 core, 550 non-core); Num. remaining: 922\n", + "Reaction no. 209\n", + "Attempting to remove reaction: HAS1 ...\n", + "Initial PM reactions: 1785\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4474230000000716\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['GLCURtly', 'PGM', 'MDH', 'GLCAASE8ly', 'L_LACt2r', 'ENO', 'GLCAASE9ly', 'CYStec', 'NACHEX27ly'], inactive_NC:['HAS2', 'HAtly', 'HAS1']\n", + "Zero-expression evidence for reaction...\n", + "1785\n", + "1785\n", + "check_model_function done ....\n", + "Len P: 922\n", + "num_removed 641\n", + "Len P AFTER 921\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 641 (91 core, 550 non-core); Num. remaining: 921\n", + "Reaction no. 210\n", + "Attempting to remove reaction: ASP1DC ...\n", + "Initial PM reactions: 1785\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4191329999998743\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['ASP1DC']\n", + "Zero-expression evidence for reaction...\n", + "1785\n", + "1785\n", + "check_model_function done ....\n", + "PM reactions (before): 1785\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1784\n", + "Num. removed: 642 (91 core, 551 non-core); Num. remaining: 920\n", + "Reaction no. 211\n", + "Attempting to remove reaction: CHLP ...\n", + "Initial PM reactions: 1784\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4110980000000382\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['CHLP']\n", + "Zero-expression evidence for reaction...\n", + "1784\n", + "1784\n", + "check_model_function done ....\n", + "PM reactions (before): 1784\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1783\n", + "Num. removed: 643 (91 core, 552 non-core); Num. remaining: 919\n", + "Reaction no. 212\n", + "Attempting to remove reaction: GLYATm ...\n", + "Initial PM reactions: 1783\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.560193999999683\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['GDHm', 'FACOAL224'], inactive_NC:['EX_adrn_e', 'THRGLYexR', 'FATP6t', 'EX_gln__L_e', 'GLYATm', 'AOBUTDsm', 'AACTtm', 'AACTOOR']\n", + "Zero-expression evidence for reaction...\n", + "1783\n", + "1783\n", + "check_model_function done ....\n", + "Len P: 919\n", + "num_removed 643\n", + "Len P AFTER 918\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 643 (91 core, 552 non-core); Num. remaining: 918\n", + "Reaction no. 213\n", + "Attempting to remove reaction: P4501B1r ...\n", + "Initial PM reactions: 1783\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.443948999999975\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['PPM', 'AKGMALtm'], inactive_NC:['ALAt2r', 'GHMT2r', 'P4501B1r', 'HESTRATRIOLtr', 'EX_hestratriol_e', 'HESTRATRIOLte']\n", + "Zero-expression evidence for reaction...\n", + "1783\n", + "1783\n", + "check_model_function done ....\n", + "Len P: 918\n", + "num_removed 643\n", + "Len P AFTER 917\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 643 (91 core, 552 non-core); Num. remaining: 917\n", + "Reaction no. 214\n", + "Attempting to remove reaction: ACACT10m ...\n", + "Initial PM reactions: 1783\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.446425999999974\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['OIVD3m', 'ACOAD10m', 'ECOAH9m', 'HACD9m'], inactive_NC:['ILETA', 'ACACT10m', '3MOPt2im']\n", + "Zero-expression evidence for reaction...\n", + "1783\n", + "1783\n", + "check_model_function done ....\n", + "Len P: 917\n", + "num_removed 643\n", + "Len P AFTER 916\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 643 (91 core, 552 non-core); Num. remaining: 916\n", + "Reaction no. 215\n", + "Attempting to remove reaction: URIt5 ...\n", + "Initial PM reactions: 1783\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4283460000001469\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PUNP1', 'ASPGLUm'], inactive_NC:['URIt5']\n", + "Zero-expression evidence for reaction...\n", + "1783\n", + "1783\n", + "check_model_function done ....\n", + "Len P: 916\n", + "num_removed 643\n", + "Len P AFTER 915\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 643 (91 core, 552 non-core); Num. remaining: 915\n", + "Reaction no. 216\n", + "Attempting to remove reaction: URIt4 ...\n", + "Initial PM reactions: 1783\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3984059999997953\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['URIt4']\n", + "Zero-expression evidence for reaction...\n", + "1783\n", + "1783\n", + "check_model_function done ....\n", + "PM reactions (before): 1783\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1782\n", + "Num. removed: 644 (91 core, 553 non-core); Num. remaining: 914\n", + "Reaction no. 217\n", + "Attempting to remove reaction: GALt4_2 ...\n", + "Initial PM reactions: 1782\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4566549999999552\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['EX_adn_e', 'GALt4_2']\n", + "Zero-expression evidence for reaction...\n", + "1782\n", + "1782\n", + "check_model_function done ....\n", + "PM reactions (before): 1782\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1780\n", + "Num. removed: 646 (91 core, 555 non-core); Num. remaining: 912\n", + "Reaction no. 218\n", + "Attempting to remove reaction: GALt4 ...\n", + "Initial PM reactions: 1780\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5706829999999172\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['EX_gln__L_e', 'PROt4_2_r', 'GALt4']\n", + "Zero-expression evidence for reaction...\n", + "1780\n", + "1780\n", + "check_model_function done ....\n", + "PM reactions (before): 1780\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1777\n", + "Num. removed: 649 (91 core, 558 non-core); Num. remaining: 910\n", + "Reaction no. 219\n", + "Attempting to remove reaction: NCCt ...\n", + "Initial PM reactions: 1777\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.449974999999995\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['CYStec'], inactive_NC:['NCCt', 'RADH', 'PROt2r']\n", + "Zero-expression evidence for reaction...\n", + "1777\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1777\n", + "check_model_function done ....\n", + "PM reactions (before): 1777\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1773\n", + "Num. removed: 653 (92 core, 561 non-core); Num. remaining: 907\n", + "Reaction no. 220\n", + "Attempting to remove reaction: ILETA ...\n", + "Initial PM reactions: 1773\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.410399000000325\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['OIVD3m', 'ACOAD10m', 'ECOAH9m', 'HACD9m'], inactive_NC:['ILETA', 'ACACT10m', '3MOPt2im']\n", + "Zero-expression evidence for reaction...\n", + "1773\n", + "1773\n", + "check_model_function done ....\n", + "Len P: 907\n", + "num_removed 653\n", + "Len P AFTER 906\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 653 (92 core, 561 non-core); Num. remaining: 906\n", + "Reaction no. 221\n", + "Attempting to remove reaction: BTNt4i ...\n", + "Initial PM reactions: 1773\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.35178599999972\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['SO4t4_3', 'BTNt4i']\n", + "Zero-expression evidence for reaction...\n", + "1773\n", + "1773\n", + "check_model_function done ....\n", + "PM reactions (before): 1773\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1771\n", + "Num. removed: 655 (92 core, 563 non-core); Num. remaining: 905\n", + "Reaction no. 222\n", + "Attempting to remove reaction: INSt5 ...\n", + "Initial PM reactions: 1771\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.37647300000026\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['INSt5']\n", + "Zero-expression evidence for reaction...\n", + "1771\n", + "1771\n", + "check_model_function done ....\n", + "PM reactions (before): 1771\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1770\n", + "Num. removed: 656 (92 core, 564 non-core); Num. remaining: 904\n", + "Reaction no. 223\n", + "Attempting to remove reaction: INSt4 ...\n", + "Initial PM reactions: 1770\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4610160000001997\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['INSt4', 'NCNt', 'THRGLNexR']\n", + "Zero-expression evidence for reaction...\n", + "1770\n", + "1770\n", + "check_model_function done ....\n", + "PM reactions (before): 1770\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1767\n", + "Num. removed: 659 (92 core, 567 non-core); Num. remaining: 902\n", + "Reaction no. 224\n", + "Attempting to remove reaction: DTMPK ...\n", + "Initial PM reactions: 1767\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 13 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5123199999998178\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 14 , inactive_C: ['NDPK4n', 'NDPK4'], inactive_NC:['DNDPt49m', 'DNDPt46m', 'DM_dttp_n', 'DNDPt47m', 'DNDPt45m', 'DNDPt50m', 'CAt7r', 'DTMPK', 'DNDPt44m', 'DNDPt48m', 'DTDPtn', 'DM_dttp_m']\n", + "Zero-expression evidence for reaction...\n", + "1767\n", + "1767\n", + "check_model_function done ....\n", + "PM reactions (before): 1767\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1753\n", + "Num. removed: 673 (94 core, 579 non-core); Num. remaining: 891\n", + "Reaction no. 225\n", + "Attempting to remove reaction: AGDC ...\n", + "Initial PM reactions: 1753\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 28 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.44537900000023\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 29 , inactive_C: ['ACNAM9PL2', 'SIAASEly', 'GALASE1ly', 'GASNASEly', 'ACNAMlt', 'AHEXASEly', 'AHEXASE2ly', 'GASNASE2ly', 'HEX4', 'A_MANASEly', 'ACGAM6PS', 'FUCASEe'], inactive_NC:['EX_ac_e', 'EX_n2m2nmasn_e', 'MANtly', 'ENGASEly', 'AGDC', 'ACt2r', 'DM_kdn_c', 'THRGLYexR', 'EX_s2l2fn2m2masn_e', 'N2M2NMASNtly', 'RADH2', 'B_MANNASEly', 'KDNH', 'S2L2N2M2MASNtly', 'DM_Asn_X_Ser_Thr_l', 'ENGASE2ly', 'GALtly']\n", + "Zero-expression evidence for reaction...\n", + "1753\n", + "1753\n", + "check_model_function done ....\n", + "Len P: 891\n", + "num_removed 673\n", + "Len P AFTER 890\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 673 (94 core, 579 non-core); Num. remaining: 890\n", + "Reaction no. 226\n", + "Attempting to remove reaction: GLYt7_211_r ...\n", + "Initial PM reactions: 1753\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3825970000002599\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['GLYt7_211_r']\n", + "Zero-expression evidence for reaction...\n", + "1753\n", + "1753\n", + "check_model_function done ....\n", + "PM reactions (before): 1753\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1752\n", + "Num. removed: 674 (94 core, 580 non-core); Num. remaining: 889\n", + "Reaction no. 227\n", + "Attempting to remove reaction: GLYt7_311_r ...\n", + "Initial PM reactions: 1752\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4296879999997145\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['THRGLYexR', 'GLYt7_311_r']\n", + "Zero-expression evidence for reaction...\n", + "1752\n", + "1752\n", + "check_model_function done ....\n", + "PM reactions (before): 1752\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1750\n", + "Num. removed: 676 (94 core, 582 non-core); Num. remaining: 888\n", + "Reaction no. 228\n", + "Attempting to remove reaction: GLYt2r ...\n", + "Initial PM reactions: 1750\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3881529999998747\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['LEUtec'], inactive_NC:['CYTK1', 'GLYt2r']\n", + "Zero-expression evidence for reaction...\n", + "1750\n", + "1750\n", + "check_model_function done ....\n", + "Len P: 888\n", + "num_removed 676\n", + "Len P AFTER 887\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 676 (94 core, 582 non-core); Num. remaining: 887\n", + "Reaction no. 229\n", + "Attempting to remove reaction: GHMT2r ...\n", + "Initial PM reactions: 1750\n", + "check_model_function done ....\n", + "Num. removed: 676 (94 core, 582 non-core); Num. remaining: 886\n", + "Reaction no. 230\n", + "Attempting to remove reaction: THMDt4 ...\n", + "Initial PM reactions: 1750\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3795489999997699\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['LEUtec', 'MTHFD2m'], inactive_NC:['THMDt4']\n", + "Zero-expression evidence for reaction...\n", + "1750\n", + "1750\n", + "check_model_function done ....\n", + "Len P: 886\n", + "num_removed 676\n", + "Len P AFTER 885\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 676 (94 core, 582 non-core); Num. remaining: 885\n", + "Reaction no. 231\n", + "Attempting to remove reaction: THMDt5 ...\n", + "Initial PM reactions: 1750\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.387492000000293\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['THMDt5']\n", + "Zero-expression evidence for reaction...\n", + "1750\n", + "1750\n", + "check_model_function done ....\n", + "PM reactions (before): 1750\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1749\n", + "Num. removed: 677 (94 core, 583 non-core); Num. remaining: 884\n", + "Reaction no. 232\n", + "Attempting to remove reaction: BTNPL ...\n", + "Initial PM reactions: 1749\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.396052999999938\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['THD1m', 'MDH', 'ASPGLUm'], inactive_NC:['BTNPL', 'APOC_LYS_BTNP', 'LYStn', 'BACCL', 'APOCF', 'BTND1n', 'BTNtn', 'BIOCYTtn', 'BTND1']\n", + "Zero-expression evidence for reaction...\n", + "1749\n", + "1749\n", + "check_model_function done ....\n", + "PM reactions (before): 1749\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1737\n", + "Num. removed: 689 (97 core, 592 non-core); Num. remaining: 875\n", + "Reaction no. 233\n", + "Attempting to remove reaction: BPNT ...\n", + "Initial PM reactions: 1737\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 52 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5580399999998917\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 53 , inactive_C: ['STS1', 'CHSTEROLSULT', 'HSD17B8r', 'TYMSULT', 'STS4', 'DOPASULT', 'SADT', 'STS2', 'STS3', '3SALAASPm', 'PRGNLONESULT', 'UGT1A6r', 'ADSK', 'SULFOX', 'ASPTAm', 'UGT1A1r', '3SALATAim', 'ESTSULT', 'ESTRADIOLGLCt2', '4NPHSULT', '3SALATAi', 'HSD17B7r'], inactive_NC:['NRPPHRSULT', 'EX_estradiolglc_e', 'EX_dopasf_e', 'EX_estrones_e', '5ADTSTSTERONESULT', 'ESTRONEGLCt', 'DHEASULT', 'FUMSO3tm', 'P4501B1r', 'HESTRATRIOLtr', '3SPYRSPm', 'DOPASFt', 'EX_estroneglc_e', 'EX_hestratriol_e', 'EX_5adtststerones_e', '4NPHSFte', 'TYMSFt', '3SPYRSP', 'ESTRONEGLCtr', '5ADTSTSTERONESte', 'ESTRONESt2', 'ESTRONEtr', 'HESTRATRIOLte', 'RADH2', 'EX_4nphsf_e', 'BPNT', '2AMACSULT', 'EX_tymsf_e', 'ESTRADIOLGLCtr', 'NRPPHRSFt', 'EX_nrpphrsf_e']\n", + "Zero-expression evidence for reaction...\n", + "1737\n", + "1737\n", + "check_model_function done ....\n", + "Len P: 875\n", + "num_removed 689\n", + "Len P AFTER 874\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 689 (97 core, 592 non-core); Num. remaining: 874\n", + "Reaction no. 234\n", + "Attempting to remove reaction: GSNt5 ...\n", + "Initial PM reactions: 1737\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3692450000003191\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['GSNt5', 'RADH2']\n", + "Zero-expression evidence for reaction...\n", + "1737\n", + "1737\n", + "check_model_function done ....\n", + "PM reactions (before): 1737\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1735\n", + "Num. removed: 691 (97 core, 594 non-core); Num. remaining: 872\n", + "Reaction no. 235\n", + "Attempting to remove reaction: GSNt4 ...\n", + "Initial PM reactions: 1735\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3561190000000352\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['NTP3e', 'LEUtec', 'NDP3ex', 'NTD9e'], inactive_NC:['GSNt4', 'EX_gtp_e']\n", + "Zero-expression evidence for reaction...\n", + "1735\n", + "1735\n", + "check_model_function done ....\n", + "Len P: 872\n", + "num_removed 691\n", + "Len P AFTER 871\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 691 (97 core, 594 non-core); Num. remaining: 871\n", + "Reaction no. 236\n", + "Attempting to remove reaction: HCO3_NAt ...\n", + "Initial PM reactions: 1735\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4276139999997213\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['FTHFLi'], inactive_NC:['HCO3_NAt']\n", + "Zero-expression evidence for reaction...\n", + "1735\n", + "1735\n", + "check_model_function done ....\n", + "Len P: 871\n", + "num_removed 691\n", + "Len P AFTER 870\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 691 (97 core, 594 non-core); Num. remaining: 870\n", + "Reaction no. 237\n", + "Attempting to remove reaction: MCCCrm ...\n", + "Initial PM reactions: 1735\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4763719999996283\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['MGCHrm', 'OIVD1m'], inactive_NC:['ACOAD8m', 'MCCCrm']\n", + "Zero-expression evidence for reaction...\n", + "1735\n", + "1735\n", + "check_model_function done ....\n", + "Len P: 870\n", + "num_removed 691\n", + "Len P AFTER 869\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 691 (97 core, 594 non-core); Num. remaining: 869\n", + "Reaction no. 238\n", + "Attempting to remove reaction: DALAt2r ...\n", + "Initial PM reactions: 1735\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.316186000000016\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['LEUtec'], inactive_NC:['ALADGLYexR', 'DALAt2r']\n", + "Zero-expression evidence for reaction...\n", + "1735\n", + "1735\n", + "check_model_function done ....\n", + "Len P: 869\n", + "num_removed 691\n", + "Len P AFTER 868\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 691 (97 core, 594 non-core); Num. remaining: 868\n", + "Reaction no. 239\n", + "Attempting to remove reaction: NH4t3r ...\n", + "Initial PM reactions: 1735\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4393199999999524\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['LEUtec', 'GTHPi'], inactive_NC:['ALAt2r', 'NH4t3r']\n", + "Zero-expression evidence for reaction...\n", + "1735\n", + "1735\n", + "check_model_function done ....\n", + "Len P: 868\n", + "num_removed 691\n", + "Len P AFTER 867\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 691 (97 core, 594 non-core); Num. remaining: 867\n", + "Reaction no. 240\n", + "Attempting to remove reaction: LACZe ...\n", + "Initial PM reactions: 1735\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3662529999996877\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['ASPTAm'], inactive_NC:['GALt2_2', 'EX_lcts_e', 'LACZe']\n", + "Zero-expression evidence for reaction...\n", + "1735\n", + "1735\n", + "check_model_function done ....\n", + "Len P: 867\n", + "num_removed 691\n", + "Len P AFTER 866\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 691 (97 core, 594 non-core); Num. remaining: 866\n", + "Reaction no. 241\n", + "Attempting to remove reaction: ICDHym ...\n", + "Initial PM reactions: 1735\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3746249999999236\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['NKCC2t', 'PGM', 'ICDHxm', 'ENO', 'GTHPi'], inactive_NC:['ICDHym']\n", + "Zero-expression evidence for reaction...\n", + "1735\n", + "1735\n", + "check_model_function done ....\n", + "Len P: 866\n", + "num_removed 691\n", + "Len P AFTER 865\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 691 (97 core, 594 non-core); Num. remaining: 865\n", + "Reaction no. 242\n", + "Attempting to remove reaction: GLUDC ...\n", + "Initial PM reactions: 1735\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4404850000000806\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['GLUDC']\n", + "Zero-expression evidence for reaction...\n", + "1735\n", + "1735\n", + "check_model_function done ....\n", + "PM reactions (before): 1735\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1734\n", + "Num. removed: 692 (97 core, 595 non-core); Num. remaining: 864\n", + "Reaction no. 243\n", + "Attempting to remove reaction: DHORTS ...\n", + "Initial PM reactions: 1734\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4329359999996996\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['OMPDC', 'ORPT'], inactive_NC:['CBPS', 'DHORD9', 'ASPCT', 'DHORTS']\n", + "Zero-expression evidence for reaction...\n", + "1734\n", + "1734\n", + "check_model_function done ....\n", + "Len P: 864\n", + "num_removed 692\n", + "Len P AFTER 863\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 692 (97 core, 595 non-core); Num. remaining: 863\n", + "Reaction no. 244\n", + "Attempting to remove reaction: RETH ...\n", + "Initial PM reactions: 1734\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3365469999998822\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['FTHFLi', 'GDHm'], inactive_NC:['RETH']\n", + "Zero-expression evidence for reaction...\n", + "1734\n", + "1734\n", + "check_model_function done ....\n", + "Len P: 863\n", + "num_removed 692\n", + "Len P AFTER 862\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 692 (97 core, 595 non-core); Num. remaining: 862\n", + "Reaction no. 245\n", + "Attempting to remove reaction: OCBTm ...\n", + "Initial PM reactions: 1734\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4557019999997465\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['ARGNm', 'CBPSam'], inactive_NC:['CITRtm', 'UREAtm', 'ARGtm', 'OCBTm']\n", + "Zero-expression evidence for reaction...\n", + "1734\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1734\n", + "check_model_function done ....\n", + "Len P: 862\n", + "num_removed 692\n", + "Len P AFTER 861\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 692 (97 core, 595 non-core); Num. remaining: 861\n", + "Reaction no. 246\n", + "Attempting to remove reaction: SERLYSNaex ...\n", + "Initial PM reactions: 1734\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3454890000002706\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['SERLYSNaex']\n", + "Zero-expression evidence for reaction...\n", + "1734\n", + "1734\n", + "check_model_function done ....\n", + "PM reactions (before): 1734\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1733\n", + "Num. removed: 693 (97 core, 596 non-core); Num. remaining: 860\n", + "Reaction no. 247\n", + "Attempting to remove reaction: INOSTO ...\n", + "Initial PM reactions: 1733\n", + "check_model_function done ....\n", + "Num. removed: 693 (97 core, 596 non-core); Num. remaining: 859\n", + "Reaction no. 248\n", + "Attempting to remove reaction: ADNt4 ...\n", + "Initial PM reactions: 1733\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.368804000000182\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['GLCt1', 'LEUtec', '2HBt2', '2HBO'], inactive_NC:['ADNt4', 'EX_2hb_e']\n", + "Zero-expression evidence for reaction...\n", + "1733\n", + "1733\n", + "check_model_function done ....\n", + "Len P: 859\n", + "num_removed 693\n", + "Len P AFTER 858\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 693 (97 core, 596 non-core); Num. remaining: 858\n", + "Reaction no. 249\n", + "Attempting to remove reaction: ADNt5 ...\n", + "Initial PM reactions: 1733\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.407807000000048\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['NDPK5m', 'FACOAL224'], inactive_NC:['CYTK1', 'ADNt5', 'FATP6t', 'EX_adrn_e']\n", + "Zero-expression evidence for reaction...\n", + "1733\n", + "1733\n", + "check_model_function done ....\n", + "Len P: 858\n", + "num_removed 693\n", + "Len P AFTER 857\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 693 (97 core, 596 non-core); Num. remaining: 857\n", + "Reaction no. 250\n", + "Attempting to remove reaction: GLCt2 ...\n", + "Initial PM reactions: 1733\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.317677999999887\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['GLCt2']\n", + "Zero-expression evidence for reaction...\n", + "1733\n", + "1733\n", + "check_model_function done ....\n", + "PM reactions (before): 1733\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1732\n", + "Num. removed: 694 (97 core, 597 non-core); Num. remaining: 856\n", + "Reaction no. 251\n", + "Attempting to remove reaction: GLCt2_2 ...\n", + "Initial PM reactions: 1732\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3381039999999302\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['EX_cgly_e', 'GLCt2_2']\n", + "Zero-expression evidence for reaction...\n", + "1732\n", + "1732\n", + "check_model_function done ....\n", + "PM reactions (before): 1732\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1730\n", + "Num. removed: 696 (97 core, 599 non-core); Num. remaining: 854\n", + "Reaction no. 252\n", + "Attempting to remove reaction: 34DHXMANDACOX_NADP ...\n", + "Initial PM reactions: 1730\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3144970000003013\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['34DHXMANDACOX', 'L_LACtm'], inactive_NC:['EX_hco3_e', 'ARTPLM1', '34DHXMANDACOX_NADP']\n", + "Zero-expression evidence for reaction...\n", + "1730\n", + "1730\n", + "check_model_function done ....\n", + "Len P: 854\n", + "num_removed 696\n", + "Len P AFTER 853\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 696 (97 core, 599 non-core); Num. remaining: 853\n", + "Reaction no. 253\n", + "Attempting to remove reaction: CYTDt5 ...\n", + "Initial PM reactions: 1730\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.333133000000089\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['LDH_L', 'AKGMALtm', 'LEUtec', 'ASPTAm'], inactive_NC:['CYTDt5']\n", + "Zero-expression evidence for reaction...\n", + "1730\n", + "1730\n", + "check_model_function done ....\n", + "Len P: 853\n", + "num_removed 696\n", + "Len P AFTER 852\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 696 (97 core, 599 non-core); Num. remaining: 852\n", + "Reaction no. 254\n", + "Attempting to remove reaction: CYTDt4 ...\n", + "Initial PM reactions: 1730\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3682330000001457\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['2HBt2', '2HBO'], inactive_NC:['CYTDt4', 'EX_2hb_e']\n", + "Zero-expression evidence for reaction...\n", + "1730\n", + "1730\n", + "check_model_function done ....\n", + "Len P: 852\n", + "num_removed 696\n", + "Len P AFTER 851\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 696 (97 core, 599 non-core); Num. remaining: 851\n", + "Reaction no. 255\n", + "Attempting to remove reaction: CYSO ...\n", + "Initial PM reactions: 1730\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3670680000000175\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['GLCt1', 'SULFOX', 'ASPTAm', '3SALATAim', '3SALATAi', '3SALAASPm'], inactive_NC:['FUMSO3tm', '3SPYRSPm', 'GLYtm', '3SALAOX', 'CYSO', '3SPYRSP']\n", + "Zero-expression evidence for reaction...\n", + "1730\n", + "1730\n", + "check_model_function done ....\n", + "Len P: 851\n", + "num_removed 696\n", + "Len P AFTER 850\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 696 (97 core, 599 non-core); Num. remaining: 850\n", + "Reaction no. 256\n", + "Attempting to remove reaction: SSALxm ...\n", + "Initial PM reactions: 1730\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.353418000000147\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['SSALxm', '4ABUTtm', 'ABTArm']\n", + "Zero-expression evidence for reaction...\n", + "1730\n", + "1730\n", + "check_model_function done ....\n", + "PM reactions (before): 1730\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1727\n", + "Num. removed: 699 (97 core, 602 non-core); Num. remaining: 847\n", + "Reaction no. 257\n", + "Attempting to remove reaction: UPPN ...\n", + "Initial PM reactions: 1727\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4267649999997047\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['DHPM1', 'PYNP2r'], inactive_NC:['UPPN', 'DURAD']\n", + "Zero-expression evidence for reaction...\n", + "1727\n", + "1727\n", + "check_model_function done ....\n", + "Len P: 847\n", + "num_removed 699\n", + "Len P AFTER 846\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 699 (97 core, 602 non-core); Num. remaining: 846\n", + "Reaction no. 258\n", + "Attempting to remove reaction: GUAD ...\n", + "Initial PM reactions: 1727\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3155269999997472\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GLCt1'], inactive_NC:['GUAD']\n", + "Zero-expression evidence for reaction...\n", + "1727\n", + "1727\n", + "check_model_function done ....\n", + "Len P: 846\n", + "num_removed 699\n", + "Len P AFTER 845\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 699 (97 core, 602 non-core); Num. remaining: 845\n", + "Reaction no. 259\n", + "Attempting to remove reaction: LPS2 ...\n", + "Initial PM reactions: 1727\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3132620000001225\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['SUCOAS1m', 'LPS3', 'L_LACt2r'], inactive_NC:['LPS2', 'GLYK']\n", + "Zero-expression evidence for reaction...\n", + "1727\n", + "1727\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Len P: 845\n", + "num_removed 699\n", + "Len P AFTER 844\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 699 (97 core, 602 non-core); Num. remaining: 844\n", + "Reaction no. 260\n", + "Attempting to remove reaction: LPS ...\n", + "Initial PM reactions: 1727\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4259980000001633\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['LPS', 'ARTCOAL3']\n", + "Zero-expression evidence for reaction...\n", + "1727\n", + "1727\n", + "check_model_function done ....\n", + "PM reactions (before): 1727\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1725\n", + "Num. removed: 701 (97 core, 604 non-core); Num. remaining: 842\n", + "Reaction no. 261\n", + "Attempting to remove reaction: P4502C8 ...\n", + "Initial PM reactions: 1725\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.357064000000264\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['GLCt1', 'LEUtec'], inactive_NC:['TAXOLte', 'HTAXOLte', 'P4502C8', 'EX_taxol_e', 'EX_htaxol_e']\n", + "Zero-expression evidence for reaction...\n", + "1725\n", + "1725\n", + "check_model_function done ....\n", + "Len P: 842\n", + "num_removed 701\n", + "Len P AFTER 841\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 701 (97 core, 604 non-core); Num. remaining: 841\n", + "Reaction no. 262\n", + "Attempting to remove reaction: P4502C19 ...\n", + "Initial PM reactions: 1725\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4645319999999629\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['LEUtec'], inactive_NC:['5HOMEPRAZOLEte', 'EX_omeprazole_e', 'P4502C19', 'EX_5homeprazole_e', 'OMEPRAZOLEte']\n", + "Zero-expression evidence for reaction...\n", + "1725\n", + "1725\n", + "check_model_function done ....\n", + "PM reactions (before): 1725\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1719\n", + "Num. removed: 707 (98 core, 609 non-core); Num. remaining: 836\n", + "Reaction no. 263\n", + "Attempting to remove reaction: P4502C9 ...\n", + "Initial PM reactions: 1719\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.348993000000064\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['GLCt1', 'FTHFLi', 'AKGMALtm'], inactive_NC:['P4502C9', 'GHMT2r', 'TOLBUTAMIDEte', '4MTOLBUTAMIDEte', 'EX_4mtolbutamide_e', 'EX_tolbutamide_e']\n", + "Zero-expression evidence for reaction...\n", + "1719\n", + "1719\n", + "check_model_function done ....\n", + "Len P: 836\n", + "num_removed 707\n", + "Len P AFTER 835\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 707 (98 core, 609 non-core); Num. remaining: 835\n", + "Reaction no. 264\n", + "Attempting to remove reaction: P4502C92 ...\n", + "Initial PM reactions: 1719\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3047660000001997\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['AKGMALtm'], inactive_NC:['CARVEOLte', 'EX_carveol_e', 'P4502C92']\n", + "Zero-expression evidence for reaction...\n", + "1719\n", + "1719\n", + "check_model_function done ....\n", + "PM reactions (before): 1719\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1715\n", + "Num. removed: 711 (99 core, 612 non-core); Num. remaining: 832\n", + "Reaction no. 265\n", + "Attempting to remove reaction: P4502C93 ...\n", + "Initial PM reactions: 1715\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3570730000001276\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['SERtN1', 'SUCOASm'], inactive_NC:['LIMNENte', 'EX_perillyl_e', 'PERILLYLte', 'EX_limnen_e', 'P4502C93']\n", + "Zero-expression evidence for reaction...\n", + "1715\n", + "1715\n", + "check_model_function done ....\n", + "Len P: 832\n", + "num_removed 711\n", + "Len P AFTER 831\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 711 (99 core, 612 non-core); Num. remaining: 831\n", + "Reaction no. 266\n", + "Attempting to remove reaction: P4502C94 ...\n", + "Initial PM reactions: 1715\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3234259999999267\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['SUCOASm'], inactive_NC:['P4502C94', 'APNNOXte', 'EX_appnn_e', 'APPNNte', 'EX_apnnox_e']\n", + "Zero-expression evidence for reaction...\n", + "1715\n", + "1715\n", + "check_model_function done ....\n", + "PM reactions (before): 1715\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1709\n", + "Num. removed: 717 (100 core, 617 non-core); Num. remaining: 826\n", + "Reaction no. 267\n", + "Attempting to remove reaction: P4502F1 ...\n", + "Initial PM reactions: 1709\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4856920000001992\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['P4502F1', 'EX_npthl_e', 'NPTHLte', 'EX_onpthl_e', 'ONPTHLte']\n", + "Zero-expression evidence for reaction...\n", + "1709\n", + "1709\n", + "check_model_function done ....\n", + "PM reactions (before): 1709\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1704\n", + "Num. removed: 722 (100 core, 622 non-core); Num. remaining: 821\n", + "Reaction no. 268\n", + "Attempting to remove reaction: P4503A5 ...\n", + "Initial PM reactions: 1704\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3411369999998897\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['AFLATOXINte', 'EX_eaflatoxin_e', 'EAFLATOXINte', 'P4503A5', 'EX_aflatoxin_e']\n", + "Zero-expression evidence for reaction...\n", + "1704\n", + "1704\n", + "check_model_function done ....\n", + "PM reactions (before): 1704\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1699\n", + "Num. removed: 727 (100 core, 627 non-core); Num. remaining: 816\n", + "Reaction no. 269\n", + "Attempting to remove reaction: FAH3 ...\n", + "Initial PM reactions: 1699\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3115689999999631\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['EX_whhdca_e', 'FAH3', 'WHHDCAte']\n", + "Zero-expression evidence for reaction...\n", + "1699\n", + "1699\n", + "check_model_function done ....\n", + "PM reactions (before): 1699\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1696\n", + "Num. removed: 730 (100 core, 630 non-core); Num. remaining: 813\n", + "Reaction no. 270\n", + "Attempting to remove reaction: FAH2 ...\n", + "Initial PM reactions: 1696\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6243630000003577\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['EX_whttdca_e', 'FAH2', 'WHTTDCAte']\n", + "Zero-expression evidence for reaction...\n", + "1696\n", + "1696\n", + "check_model_function done ....\n", + "PM reactions (before): 1696\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1693\n", + "Num. removed: 733 (100 core, 633 non-core); Num. remaining: 810\n", + "Reaction no. 271\n", + "Attempting to remove reaction: CITt4_2 ...\n", + "Initial PM reactions: 1693\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6339909999996962\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['NDPK5m'], inactive_NC:['EX_cit_e', 'CITt4_2']\n", + "Zero-expression evidence for reaction...\n", + "1693\n", + "1693\n", + "check_model_function done ....\n", + "Len P: 810\n", + "num_removed 733\n", + "Len P AFTER 809\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 733 (100 core, 633 non-core); Num. remaining: 809\n", + "Reaction no. 272\n", + "Attempting to remove reaction: 2OXOADOXm ...\n", + "Initial PM reactions: 1693\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 16 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7082730000001902\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 17 , inactive_C: ['GLUTCOADHm', 'SACCD4m', 'LPCOXp', 'SACCD3m'], inactive_NC:['THP2Ctp', 'AASAD3m', '2AMADPTm', 'AASAD3', '1PPDCRp', 'LYStm', '2OXOADOXm', 'PPD2CSPp', 'LYStip', 'LYSOXp', 'AADSACYCL', '2OXOADPTm', 'AATA']\n", + "Zero-expression evidence for reaction...\n", + "1693\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1693\n", + "check_model_function done ....\n", + "PM reactions (before): 1693\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1676\n", + "Num. removed: 750 (104 core, 646 non-core); Num. remaining: 796\n", + "Reaction no. 273\n", + "Attempting to remove reaction: SPHK21c ...\n", + "Initial PM reactions: 1676\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3110889999998108\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['SBPP3er', 'MTHFD2m'], inactive_NC:['SPHS1Ptr', 'SPHK21c', 'SPHINGStr']\n", + "Zero-expression evidence for reaction...\n", + "1676\n", + "1676\n", + "check_model_function done ....\n", + "Len P: 796\n", + "num_removed 750\n", + "Len P AFTER 795\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 750 (104 core, 646 non-core); Num. remaining: 795\n", + "Reaction no. 274\n", + "Attempting to remove reaction: DRBK ...\n", + "Initial PM reactions: 1676\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3559620000000905\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['DADAe', 'PUNP6', 'DADA'], inactive_NC:['DRBK', '2DR1PP', 'DINt', 'DRPA']\n", + "Zero-expression evidence for reaction...\n", + "1676\n", + "1676\n", + "check_model_function done ....\n", + "Len P: 795\n", + "num_removed 750\n", + "Len P AFTER 794\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 750 (104 core, 646 non-core); Num. remaining: 794\n", + "Reaction no. 275\n", + "Attempting to remove reaction: SLCBK1 ...\n", + "Initial PM reactions: 1676\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3196349999998347\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['OCOAT1m', 'SERtN1', 'SBPP1er'], inactive_NC:['SPH1Pter', 'SLCBK1', 'SPHGNtr']\n", + "Zero-expression evidence for reaction...\n", + "1676\n", + "1676\n", + "check_model_function done ....\n", + "Len P: 794\n", + "num_removed 750\n", + "Len P AFTER 793\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 750 (104 core, 646 non-core); Num. remaining: 793\n", + "Reaction no. 276\n", + "Attempting to remove reaction: PYDAMK ...\n", + "Initial PM reactions: 1676\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5872079999999187\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['LDH_Lm'], inactive_NC:['EX_ade_e', 'PYDAMK', 'ADEt']\n", + "Zero-expression evidence for reaction...\n", + "1676\n", + "1676\n", + "check_model_function done ....\n", + "PM reactions (before): 1676\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1672\n", + "Num. removed: 754 (105 core, 649 non-core); Num. remaining: 791\n", + "Reaction no. 277\n", + "Attempting to remove reaction: MMSAD1m ...\n", + "Initial PM reactions: 1672\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2713960000000952\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['FTHFLi'], inactive_NC:['MMSAD1m']\n", + "Zero-expression evidence for reaction...\n", + "1672\n", + "1672\n", + "check_model_function done ....\n", + "Len P: 791\n", + "num_removed 754\n", + "Len P AFTER 790\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 754 (105 core, 649 non-core); Num. remaining: 790\n", + "Reaction no. 278\n", + "Attempting to remove reaction: ALAt2r ...\n", + "Initial PM reactions: 1672\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3584649999997964\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['FACOAL224'], inactive_NC:['EX_hco3_e', 'ALAt2r', 'FATP6t', 'EX_adrn_e']\n", + "Zero-expression evidence for reaction...\n", + "1672\n", + "1672\n", + "check_model_function done ....\n", + "PM reactions (before): 1672\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1667\n", + "Num. removed: 759 (106 core, 653 non-core); Num. remaining: 787\n", + "Reaction no. 279\n", + "Attempting to remove reaction: ASPCT ...\n", + "Initial PM reactions: 1667\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3522259999999733\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['OMPDC', 'GLNtN1', 'ORPT'], inactive_NC:['CBPS', 'DHORD9', 'ASPCT', 'DHORTS']\n", + "Zero-expression evidence for reaction...\n", + "1667\n", + "1667\n", + "check_model_function done ....\n", + "Len P: 787\n", + "num_removed 759\n", + "Len P AFTER 786\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 759 (106 core, 653 non-core); Num. remaining: 786\n", + "Reaction no. 280\n", + "Attempting to remove reaction: PYDXNK ...\n", + "Initial PM reactions: 1667\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3087169999998878\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['PYDXNK']\n", + "Zero-expression evidence for reaction...\n", + "1667\n", + "1667\n", + "check_model_function done ....\n", + "PM reactions (before): 1667\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1666\n", + "Num. removed: 760 (106 core, 654 non-core); Num. remaining: 785\n", + "Reaction no. 281\n", + "Attempting to remove reaction: MMCDm ...\n", + "Initial PM reactions: 1666\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3400489999999081\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['ASPTAm'], inactive_NC:['MMCDm']\n", + "Zero-expression evidence for reaction...\n", + "1666\n", + "1666\n", + "check_model_function done ....\n", + "Len P: 785\n", + "num_removed 760\n", + "Len P AFTER 784\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 760 (106 core, 654 non-core); Num. remaining: 784\n", + "Reaction no. 282\n", + "Attempting to remove reaction: PYDXK ...\n", + "Initial PM reactions: 1666\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3410909999997784\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['PDX5POi', 'PYAM5PO'], inactive_NC:['PYDXK', 'HYPOE', 'EX_cit_e', 'PYDXPP', 'PDXPP', 'CITt4_2', 'EX_pydxn_e', 'PYDXNtr', 'PYDAMtr', 'EX_pydam_e']\n", + "Zero-expression evidence for reaction...\n", + "1666\n", + "1666\n", + "check_model_function done ....\n", + "PM reactions (before): 1666\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1654\n", + "Num. removed: 772 (108 core, 664 non-core); Num. remaining: 775\n", + "Reaction no. 283\n", + "Attempting to remove reaction: GALt2_2 ...\n", + "Initial PM reactions: 1654\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3662880000001678\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['GLNtN1'], inactive_NC:['GALt2_2', 'EX_lcts_e', 'LACZe']\n", + "Zero-expression evidence for reaction...\n", + "1654\n", + "1654\n", + "check_model_function done ....\n", + "PM reactions (before): 1654\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1650\n", + "Num. removed: 776 (109 core, 667 non-core); Num. remaining: 773\n", + "Reaction no. 284\n", + "Attempting to remove reaction: NNATr_copy1 ...\n", + "Initial PM reactions: 1650\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5330699999999524\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['NNATr_copy2', 'NNATr_copy1']\n", + "Zero-expression evidence for reaction...\n", + "1650\n", + "1650\n", + "check_model_function done ....\n", + "PM reactions (before): 1650\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1648\n", + "Num. removed: 778 (109 core, 669 non-core); Num. remaining: 771\n", + "Reaction no. 285\n", + "Attempting to remove reaction: NMNAT ...\n", + "Initial PM reactions: 1648\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5618009999998321\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PUNP1'], inactive_NC:['CYTK1', 'NMNAT']\n", + "Zero-expression evidence for reaction...\n", + "1648\n", + "1648\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Len P: 771\n", + "num_removed 778\n", + "Len P AFTER 770\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 778 (109 core, 669 non-core); Num. remaining: 770\n", + "Reaction no. 286\n", + "Attempting to remove reaction: MMSAD3m ...\n", + "Initial PM reactions: 1648\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5848829999999907\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['MMSAD3m', 'APAT2rm', 'BALAtmr']\n", + "Zero-expression evidence for reaction...\n", + "1648\n", + "1648\n", + "check_model_function done ....\n", + "PM reactions (before): 1648\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1645\n", + "Num. removed: 781 (109 core, 672 non-core); Num. remaining: 767\n", + "Reaction no. 287\n", + "Attempting to remove reaction: MTHFR3 ...\n", + "Initial PM reactions: 1645\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.624652999999853\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['5MTHFt', 'METS', 'PUNP1', 'FOLR2'], inactive_NC:['FOLt2', 'PIt2m', 'DHPR2', 'EX_5mthf_e', 'EX_fol_e', 'MTHFR3']\n", + "Zero-expression evidence for reaction...\n", + "1645\n", + "1645\n", + "check_model_function done ....\n", + "Len P: 767\n", + "num_removed 781\n", + "Len P AFTER 766\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 781 (109 core, 672 non-core); Num. remaining: 766\n", + "Reaction no. 288\n", + "Attempting to remove reaction: H2Ot ...\n", + "Initial PM reactions: 1645\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4840519999997923\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['H2Ot']\n", + "Zero-expression evidence for reaction...\n", + "1645\n", + "1645\n", + "check_model_function done ....\n", + "PM reactions (before): 1645\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1644\n", + "Num. removed: 782 (109 core, 673 non-core); Num. remaining: 765\n", + "Reaction no. 289\n", + "Attempting to remove reaction: PRDXl ...\n", + "Initial PM reactions: 1644\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 125 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9399500000004082\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 126 , inactive_C: ['UDPDOLPT_U', 'GGH_7DHFl', 'GLDBRAN', 'GGH_5DHFl', 'FPGSm', 'AHEXASE2ly', 'GGNG', 'GBA', 'GALKr', 'FPGS8', 'FPGS7', 'UDPDOLPT_L', 'FPGS6', 'GLGNS1', 'NACHEX27ly', 'FPGS3', 'UGCG', 'FPGS4m', 'GGH_10FTHF5GLUl', 'PPM', 'FPGS9', 'GLUt2m', 'FPGS', 'FPGS5m', 'GGH_10FTHF7GLUl', 'GLCURtly', 'GGH_7THFl', 'FPGS5', 'CERT1rt', 'GGH_5THFl', 'GLPASE2', 'FPGS2', 'GLCAASE8ly', 'GLBRAN', 'FPGS3m', 'FPGS4', 'FPGS7m', 'UGLT', 'GLPASE1', 'MTHFCm', 'GASNASEly', 'GASNASE2ly', 'UDPGD', 'FPGS2m', 'HEX4', 'GLCAASE9ly', 'A_MANASEly', 'GGH_6DHFl', 'FUCASEe', 'ACNAM9PL2', 'SIAASEly', 'GALASE1ly', 'FPGS8m', 'GGH_10FTHF6GLUl', 'CERT2rt', 'FPGS9m', 'FPGS6m', 'GGH_6THFl', 'AHEXASEly', 'ACNAMlt'], inactive_NC:['H2O2tly', 'ENGASEly', 'MANtly', 'SARCStm', 'DOLPH_Ler', 'EX_n2m2nmasn_e', '5DHFtl', 'DM_kdn_c', 'HAS2', '10FTHF6GLUtl', 'DOLGPP_Uer', 'SARDHm', 'DOLGLCP_Uter', 'THFtm', 'DOLP_Uter', 'NDP7er', '7DHFtl', '7DHFtm', '10FTHF7GLUtm', 'KDNH', 'DHFtm', '10FTHF6GLUtm', '6THFtl', 'DOLICHOL_Uter', '7THFtl', '5THFtm', 'GLUt7l', 'HAtly', 'PRDXl', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'GUR1PP', 'DOLGPP_Ler', 'UDPG4E', 'ENGASE2ly', 'GALtly', 'DOLP_Lter', 'UDPG1P', 'DOLK_U', '6DHFtm', '10FTHF5GLUtl', 'DHFtl', 'EX_s2l2fn2m2masn_e', 'MEOHtly', 'THFtl', 'SARCStex', '6DHFtl', 'N2M2NMASNtly', 'DOLGLCP_Lter', '10FTHF5GLUtm', 'ATPasel', 'B_MANNASEly', '10FTHF7GLUtl', 'UDPGLCter', 'UDPGNP', '5THFtl', 'DOLPH_Uer', 'DOLK_L', '10FTHFtl', '6THFtm', '7THFtm', 'ACGAMtly', 'EX_sarcs_e', 'HAS1', 'FALDtly', 'DM_Asn_X_Ser_Thr_l']\n", + "Zero-expression evidence for reaction...\n", + "1644\n", + "1644\n", + "check_model_function done ....\n", + "Len P: 765\n", + "num_removed 782\n", + "Len P AFTER 764\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 782 (109 core, 673 non-core); Num. remaining: 764\n", + "Reaction no. 290\n", + "Attempting to remove reaction: ACCOALm ...\n", + "Initial PM reactions: 1644\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6120930000001863\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['GLCt1'], inactive_NC:['PPAtm', 'ACCOALm']\n", + "Zero-expression evidence for reaction...\n", + "1644\n", + "1644\n", + "check_model_function done ....\n", + "Len P: 764\n", + "num_removed 782\n", + "Len P AFTER 763\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 782 (109 core, 673 non-core); Num. remaining: 763\n", + "Reaction no. 291\n", + "Attempting to remove reaction: PIt7_copy1 ...\n", + "Initial PM reactions: 1644\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4552220000000489\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['PIt7_copy1']\n", + "Zero-expression evidence for reaction...\n", + "1644\n", + "1644\n", + "check_model_function done ....\n", + "PM reactions (before): 1644\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1643\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 762\n", + "Reaction no. 292\n", + "Attempting to remove reaction: PIt7_copy2 ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6036519999997836\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['FTHFLi', 'MTHFC', 'PUNP1', 'MTHFD'], inactive_NC:['PGK', 'PIt7_copy2', 'EX_gly_e']\n", + "Zero-expression evidence for reaction...\n", + "1643\n", + "1643\n", + "check_model_function done ....\n", + "Len P: 762\n", + "num_removed 783\n", + "Len P AFTER 761\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 761\n", + "Reaction no. 293\n", + "Attempting to remove reaction: PIt9 ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5298090000001139\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['MTHFD2m'], inactive_NC:['PIt9']\n", + "Zero-expression evidence for reaction...\n", + "1643\n", + "1643\n", + "check_model_function done ....\n", + "Len P: 761\n", + "num_removed 783\n", + "Len P AFTER 760\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 760\n", + "Reaction no. 294\n", + "Attempting to remove reaction: DNADDP ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5797229999998308\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['SERtN1', 'NDPK5m', 'ASPTAm', 'NNATn'], inactive_NC:['DNADtn', 'DNADDP', 'NICRNTtn']\n", + "Zero-expression evidence for reaction...\n", + "1643\n", + "1643\n", + "check_model_function done ....\n", + "Len P: 760\n", + "num_removed 783\n", + "Len P AFTER 759\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 759\n", + "Reaction no. 295\n", + "Attempting to remove reaction: C3STKR2r ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 95 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6781599999999344\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 96 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'PCHOLPr_hs', 'PGPP_hs', 'PSFLIP', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'EX_ps_hs_e', 'XOLTRI25te', 'NDP8', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Zero-expression evidence for reaction...\n", + "1643\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1643\n", + "check_model_function done ....\n", + "Len P: 759\n", + "num_removed 783\n", + "Len P AFTER 758\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 758\n", + "Reaction no. 296\n", + "Attempting to remove reaction: FACOAL40im ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2950510000000577\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['BUTt2r', 'GDHm', 'HACD1m', 'ACOAD1fm', 'SERtN1', 'BUTt2m', 'ECOAH1m'], inactive_NC:['EX_but_e', 'FACOAL40im']\n", + "Zero-expression evidence for reaction...\n", + "1643\n", + "1643\n", + "check_model_function done ....\n", + "Len P: 758\n", + "num_removed 783\n", + "Len P AFTER 757\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 757\n", + "Reaction no. 297\n", + "Attempting to remove reaction: KHK2 ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.319007000000056\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['GCALDD', 'FBA4', 'PPM', 'GLUt2m', 'GLXO1'], inactive_NC:['PIt9', 'KHK2', 'EX_oxa_e']\n", + "Zero-expression evidence for reaction...\n", + "1643\n", + "1643\n", + "check_model_function done ....\n", + "Len P: 757\n", + "num_removed 783\n", + "Len P AFTER 756\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 756\n", + "Reaction no. 298\n", + "Attempting to remove reaction: ACSm ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.340349999999944\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['ALDD2xm'], inactive_NC:['ACALDtm', 'ACSm', 'GHMT2r']\n", + "Zero-expression evidence for reaction...\n", + "1643\n", + "1643\n", + "check_model_function done ....\n", + "Len P: 756\n", + "num_removed 783\n", + "Len P AFTER 755\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 755\n", + "Reaction no. 299\n", + "Attempting to remove reaction: XYLK ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 754\n", + "Reaction no. 300\n", + "Attempting to remove reaction: G3PD1ir ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 35 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3803330000000642\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 36 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'G3PD2m', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'DCYTD', 'RNDR4'], inactive_NC:['CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'PCHOLPr_hs', 'PGPP_hs', 'PSFLIP', 'DUMPtn', 'G3PD1ir', 'PEFLIP', 'L_LACt4r', 'EX_ps_hs_e', 'NDP8', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'NDP6']\n", + "Zero-expression evidence for reaction...\n", + "1643\n", + "1643\n", + "check_model_function done ....\n", + "Len P: 754\n", + "num_removed 783\n", + "Len P AFTER 753\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 753\n", + "Reaction no. 301\n", + "Attempting to remove reaction: KHK ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3040329999998903\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['FBA2'], inactive_NC:['KHK', 'TRIOK']\n", + "Zero-expression evidence for reaction...\n", + "1643\n", + "1643\n", + "check_model_function done ....\n", + "Len P: 753\n", + "num_removed 783\n", + "Len P AFTER 752\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 752\n", + "Reaction no. 302\n", + "Attempting to remove reaction: FADDP ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.29863800000021\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['LEUTAm', 'FMNAT'], inactive_NC:['LEUt5m', 'FADDP']\n", + "Zero-expression evidence for reaction...\n", + "1643\n", + "1643\n", + "check_model_function done ....\n", + "Len P: 752\n", + "num_removed 783\n", + "Len P AFTER 751\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 751\n", + "Reaction no. 303\n", + "Attempting to remove reaction: CRNtHa ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5791839999997137\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PIt8', 'CRNtuNa'], inactive_NC:['CRNtHa']\n", + "Zero-expression evidence for reaction...\n", + "1643\n", + "1643\n", + "check_model_function done ....\n", + "Len P: 751\n", + "num_removed 783\n", + "Len P AFTER 750\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 783 (109 core, 674 non-core); Num. remaining: 750\n", + "Reaction no. 304\n", + "Attempting to remove reaction: NOS2 ...\n", + "Initial PM reactions: 1643\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5701789999998255\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['NOt', 'NOS2', 'EX_no_e', 'PIt9', 'NOS1']\n", + "Zero-expression evidence for reaction...\n", + "1643\n", + "1643\n", + "check_model_function done ....\n", + "PM reactions (before): 1643\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1638\n", + "Num. removed: 788 (109 core, 679 non-core); Num. remaining: 746\n", + "Reaction no. 305\n", + "Attempting to remove reaction: CSNATm ...\n", + "Initial PM reactions: 1638\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5887259999999515\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['ACRNtm'], inactive_NC:['CSNATr', 'CSNATm']\n", + "Zero-expression evidence for reaction...\n", + "1638\n", + "1638\n", + "check_model_function done ....\n", + "Len P: 746\n", + "num_removed 788\n", + "Len P AFTER 745\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 788 (109 core, 679 non-core); Num. remaining: 745\n", + "Reaction no. 306\n", + "Attempting to remove reaction: UDPGP ...\n", + "Initial PM reactions: 1638\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5330189999999675\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['UDPGP', 'CO2tm']\n", + "Zero-expression evidence for reaction...\n", + "1638\n", + "1638\n", + "check_model_function done ....\n", + "PM reactions (before): 1638\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1636\n", + "Num. removed: 790 (109 core, 681 non-core); Num. remaining: 743\n", + "Reaction no. 307\n", + "Attempting to remove reaction: CYOOm3 ...\n", + "Initial PM reactions: 1636\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 21 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6004519999996774\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 22 , inactive_C: ['OMPDC', 'SULFOX', 'ASPTAm', 'ORPT', 'SPODMm', '3SALATAim', 'ETF', '3SALATAi', '3SALAASPm'], inactive_NC:['CBPS', 'EX_pi_e', 'FUMSO3tm', 'DHORD9', 'ASPCT', 'L_LACDcm', '3SPYRSPm', 'NADH2_u10m', 'CYOOm3', 'DHORTS', 'CYOR_u10m', 'ETFQO', '3SPYRSP']\n", + "Zero-expression evidence for reaction...\n", + "1636\n", + "1636\n", + "check_model_function done ....\n", + "Len P: 743\n", + "num_removed 790\n", + "Len P AFTER 742\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 790 (109 core, 681 non-core); Num. remaining: 742\n", + "Reaction no. 308\n", + "Attempting to remove reaction: HKt ...\n", + "Initial PM reactions: 1636\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.534624999999778\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['GLCt1', 'PPM', 'FTHFLi', 'GDHm'], inactive_NC:['EX_lac__L_e', 'HKt']\n", + "Zero-expression evidence for reaction...\n", + "1636\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1636\n", + "check_model_function done ....\n", + "Len P: 742\n", + "num_removed 790\n", + "Len P AFTER 741\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 790 (109 core, 681 non-core); Num. remaining: 741\n", + "Reaction no. 309\n", + "Attempting to remove reaction: BILDGLCURte ...\n", + "Initial PM reactions: 1636\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.207271000000219\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['BILDGLCURte']\n", + "Zero-expression evidence for reaction...\n", + "1636\n", + "1636\n", + "check_model_function done ....\n", + "PM reactions (before): 1636\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1635\n", + "Num. removed: 791 (109 core, 682 non-core); Num. remaining: 740\n", + "Reaction no. 310\n", + "Attempting to remove reaction: BILGLCURte ...\n", + "Initial PM reactions: 1635\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 32 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.407419000000118\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 33 , inactive_C: ['KCC2t', 'UGT1A10r', 'UGT1A5r', 'UGT1A6r', 'UGT1A1r', 'UGT1A2r', 'UGT1A5r2', 'ESTRADIOLGLCt2'], inactive_NC:['BILDGLCURt', 'RETNtr', 'RETNGLCt2', 'BILGLCURte', 'EX_estradiolglc_e', 'BILGLCURtr', 'BILIRUBtr', 'EX_retnglc_e', 'ESTRONEGLCt', '5ADTSTSTERONEGLCtr', 'EX_estroneglc_e', 'EX_13_cis_retnglc_e', 'UGT1A9r', '5ADTSTSTERONEtr', 'ESTRONEGLCtr', 'RETNGLCt', 'RETNtr2', 'RETNGLCtr', 'RETNGLCt2r', 'EX_bildglcur_e', '5ADTSTSTERONEGLCte', 'ESTRADIOLGLCtr', 'EX_bilglcur_e', 'BILDGLCURtr', 'EX_5adtststeroneglc_e']\n", + "Zero-expression evidence for reaction...\n", + "1635\n", + "1635\n", + "check_model_function done ....\n", + "PM reactions (before): 1635\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1602\n", + "Num. removed: 824 (117 core, 707 non-core); Num. remaining: 717\n", + "Reaction no. 311\n", + "Attempting to remove reaction: BALAVECSEC ...\n", + "Initial PM reactions: 1602\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2604899999996633\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['DHPM1', 'BAMPPALDOX', 'PYNP2r'], inactive_NC:['EX_ala_B_e', '13DAMPPOX', 'BALAVECSEC', 'SPMDOX', 'UPPN', 'DURAD']\n", + "Zero-expression evidence for reaction...\n", + "1602\n", + "1602\n", + "check_model_function done ....\n", + "Len P: 717\n", + "num_removed 824\n", + "Len P AFTER 716\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 824 (117 core, 707 non-core); Num. remaining: 716\n", + "Reaction no. 312\n", + "Attempting to remove reaction: ADRNLPVESSEC ...\n", + "Initial PM reactions: 1602\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.243815999999697\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GTHPi'], inactive_NC:['EX_ac_e', 'ADRNLPVESSEC', 'ACt2r', 'EX_adrnl_e']\n", + "Zero-expression evidence for reaction...\n", + "1602\n", + "1602\n", + "check_model_function done ....\n", + "PM reactions (before): 1602\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1597\n", + "Num. removed: 829 (118 core, 711 non-core); Num. remaining: 712\n", + "Reaction no. 313\n", + "Attempting to remove reaction: GABAVESSEC ...\n", + "Initial PM reactions: 1597\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2649970000002213\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['ABUTD', 'BAMPPALDOX'], inactive_NC:['13DAMPPOX', 'EX_4abut_e', 'SPMDOX', 'PTRCOX1', 'GABAVESSEC']\n", + "Zero-expression evidence for reaction...\n", + "1597\n", + "1597\n", + "check_model_function done ....\n", + "Len P: 712\n", + "num_removed 829\n", + "Len P AFTER 711\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 829 (118 core, 711 non-core); Num. remaining: 711\n", + "Reaction no. 314\n", + "Attempting to remove reaction: 5HTRPVESSEC ...\n", + "Initial PM reactions: 1597\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3719380000002275\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['PPM', 'FTHFLi', 'MTHFC', 'MTHFD'], inactive_NC:['EX_5htrp_e', '5HTRPVESSEC', 'TRPHYDRO2', 'EX_gly_e']\n", + "Zero-expression evidence for reaction...\n", + "1597\n", + "1597\n", + "check_model_function done ....\n", + "Len P: 711\n", + "num_removed 829\n", + "Len P AFTER 710\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 829 (118 core, 711 non-core); Num. remaining: 710\n", + "Reaction no. 315\n", + "Attempting to remove reaction: NDP8 ...\n", + "Initial PM reactions: 1597\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2178220000000692\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['NDP8']\n", + "Zero-expression evidence for reaction...\n", + "1597\n", + "1597\n", + "check_model_function done ....\n", + "PM reactions (before): 1597\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1596\n", + "Num. removed: 830 (118 core, 712 non-core); Num. remaining: 709\n", + "Reaction no. 316\n", + "Attempting to remove reaction: GLYVESSEC ...\n", + "Initial PM reactions: 1596\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2438079999997171\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['GLYVESSEC']\n", + "Zero-expression evidence for reaction...\n", + "1596\n", + "1596\n", + "check_model_function done ....\n", + "PM reactions (before): 1596\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1595\n", + "Num. removed: 831 (118 core, 713 non-core); Num. remaining: 708\n", + "Reaction no. 317\n", + "Attempting to remove reaction: HMGCOASm ...\n", + "Initial PM reactions: 1595\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2176179999996748\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['L_LACt4r', 'HMGCOASm']\n", + "Zero-expression evidence for reaction...\n", + "1595\n", + "1595\n", + "check_model_function done ....\n", + "PM reactions (before): 1595\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1593\n", + "Num. removed: 833 (118 core, 715 non-core); Num. remaining: 706\n", + "Reaction no. 318\n", + "Attempting to remove reaction: PEFLIP ...\n", + "Initial PM reactions: 1593\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 31 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6175310000003265\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 32 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'DCYTD', 'RNDR4'], inactive_NC:['THMDt4', 'NDP6', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'PSFLIP', 'PEFLIP', 'EX_ps_hs_e', 'AHCYStr']\n", + "Zero-expression evidence for reaction...\n", + "1593\n", + "1593\n", + "check_model_function done ....\n", + "Len P: 706\n", + "num_removed 833\n", + "Len P AFTER 705\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 833 (118 core, 715 non-core); Num. remaining: 705\n", + "Reaction no. 319\n", + "Attempting to remove reaction: NAt3_1 ...\n", + "Initial PM reactions: 1593\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.46119200000021\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['NAt3_1']\n", + "Zero-expression evidence for reaction...\n", + "1593\n", + "1593\n", + "check_model_function done ....\n", + "PM reactions (before): 1593\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1592\n", + "Num. removed: 834 (118 core, 716 non-core); Num. remaining: 704\n", + "Reaction no. 320\n", + "Attempting to remove reaction: CYOR_u10m ...\n", + "Initial PM reactions: 1592\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5925240000001395\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['OMPDC', 'ETF', 'ORPT'], inactive_NC:['CBPS', 'DHORD9', 'ASPCT', 'NADH2_u10m', 'MALSO4tm', 'DHORTS', 'CYOR_u10m', 'FUMSO4tm', 'ETFQO']\n", + "Zero-expression evidence for reaction...\n", + "1592\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1592\n", + "check_model_function done ....\n", + "Len P: 704\n", + "num_removed 834\n", + "Len P AFTER 703\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 834 (118 core, 716 non-core); Num. remaining: 703\n", + "Reaction no. 321\n", + "Attempting to remove reaction: ARGN ...\n", + "Initial PM reactions: 1592\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4619149999998626\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['ARGN']\n", + "Zero-expression evidence for reaction...\n", + "1592\n", + "1592\n", + "check_model_function done ....\n", + "PM reactions (before): 1592\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1591\n", + "Num. removed: 835 (118 core, 717 non-core); Num. remaining: 702\n", + "Reaction no. 322\n", + "Attempting to remove reaction: HGNTOR ...\n", + "Initial PM reactions: 1591\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5311430000001565\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['FUMAC', 'MACACI', 'TYRTA', 'AACOAT'], inactive_NC:['34HPPOR', 'HGNTOR']\n", + "Zero-expression evidence for reaction...\n", + "1591\n", + "1591\n", + "check_model_function done ....\n", + "Len P: 702\n", + "num_removed 835\n", + "Len P AFTER 701\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 835 (118 core, 717 non-core); Num. remaining: 701\n", + "Reaction no. 323\n", + "Attempting to remove reaction: RBK ...\n", + "Initial PM reactions: 1591\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3278100000002269\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['PPM'], inactive_NC:['EX_rib__D_e', 'RIBt2', 'RBK']\n", + "Zero-expression evidence for reaction...\n", + "1591\n", + "1591\n", + "check_model_function done ....\n", + "PM reactions (before): 1591\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1587\n", + "Num. removed: 839 (119 core, 720 non-core); Num. remaining: 698\n", + "Reaction no. 324\n", + "Attempting to remove reaction: DOPAVESSEC ...\n", + "Initial PM reactions: 1587\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2403189999999995\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['EX_dopa_e', 'DOPAVESSEC']\n", + "Zero-expression evidence for reaction...\n", + "1587\n", + "1587\n", + "check_model_function done ....\n", + "PM reactions (before): 1587\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1585\n", + "Num. removed: 841 (119 core, 722 non-core); Num. remaining: 696\n", + "Reaction no. 325\n", + "Attempting to remove reaction: PSFLIP ...\n", + "Initial PM reactions: 1585\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2377580000002126\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['FTHFLi', 'MTHFC', 'PUNP1', 'MTHFD'], inactive_NC:['PSFLIP', 'EX_ps_hs_e']\n", + "Zero-expression evidence for reaction...\n", + "1585\n", + "1585\n", + "check_model_function done ....\n", + "Len P: 696\n", + "num_removed 841\n", + "Len P AFTER 695\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 841 (119 core, 722 non-core); Num. remaining: 695\n", + "Reaction no. 326\n", + "Attempting to remove reaction: HISTAVESSEC ...\n", + "Initial PM reactions: 1585\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2259890000000269\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['ENO', 'PGM'], inactive_NC:['HISTAVESSEC', '3HCO3_NAt', 'GLYt2r', 'HISTAtu']\n", + "Zero-expression evidence for reaction...\n", + "1585\n", + "1585\n", + "check_model_function done ....\n", + "Len P: 695\n", + "num_removed 841\n", + "Len P AFTER 694\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 841 (119 core, 722 non-core); Num. remaining: 694\n", + "Reaction no. 327\n", + "Attempting to remove reaction: ACOAH ...\n", + "Initial PM reactions: 1585\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2506660000003649\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['ENO', 'NKCC2t', 'PUNP1', 'PGM'], inactive_NC:['EX_pi_e', 'ACOAH', 'GLYt2r', '2HCO3_NAt']\n", + "Zero-expression evidence for reaction...\n", + "1585\n", + "1585\n", + "check_model_function done ....\n", + "Len P: 694\n", + "num_removed 841\n", + "Len P AFTER 693\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 841 (119 core, 722 non-core); Num. remaining: 693\n", + "Reaction no. 328\n", + "Attempting to remove reaction: NADH2_u10m ...\n", + "Initial PM reactions: 1585\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1726259999995818\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['NADH2_u10m']\n", + "Zero-expression evidence for reaction...\n", + "1585\n", + "1585\n", + "check_model_function done ....\n", + "PM reactions (before): 1585\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1584\n", + "Num. removed: 842 (119 core, 723 non-core); Num. remaining: 692\n", + "Reaction no. 329\n", + "Attempting to remove reaction: OPAH ...\n", + "Initial PM reactions: 1584\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.245227000000341\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['AMPTASECGe', 'PGM', 'CGLYt3_2', 'ENO', 'AMPTASECG', 'GTHS'], inactive_NC:['GLUCYS', 'HCO3_NAt', 'GGLUCT', 'GTMLTe', 'OPAH']\n", + "Zero-expression evidence for reaction...\n", + "1584\n", + "1584\n", + "check_model_function done ....\n", + "Len P: 692\n", + "num_removed 842\n", + "Len P AFTER 691\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 842 (119 core, 723 non-core); Num. remaining: 691\n", + "Reaction no. 330\n", + "Attempting to remove reaction: ASPt6 ...\n", + "Initial PM reactions: 1584\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.189976999999999\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['ASPt6', 'EX_asp__L_e']\n", + "Zero-expression evidence for reaction...\n", + "1584\n", + "1584\n", + "check_model_function done ....\n", + "PM reactions (before): 1584\n", + "Removed all inactive reactions\n", + "PM reactions (after): 1582\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 689\n", + "Reaction no. 331\n", + "Attempting to remove reaction: GLUCYS ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2356300000001283\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['AMPTASECG', 'AMPTASECGe', 'GTHS', 'CGLYt3_2'], inactive_NC:['GLUCYS', 'GGLUCT', 'GTMLTe', 'GLYt2r', 'OPAH']\n", + "Zero-expression evidence for reaction...\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "Len P: 689\n", + "num_removed 844\n", + "Len P AFTER 688\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 688\n", + "Reaction no. 332\n", + "Attempting to remove reaction: AKGDm ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2808690000001661\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['SERtN1', 'PUNP1'], inactive_NC:['AKGDm']\n", + "Zero-expression evidence for reaction...\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "Len P: 688\n", + "num_removed 844\n", + "Len P AFTER 687\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 687\n", + "Reaction no. 333\n", + "Attempting to remove reaction: ATPS4m ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2701670000001286\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GLCt1'], inactive_NC:['MALSO4tm', 'FUMSO4tm', 'EX_gly_e', 'ATPS4m']\n", + "Zero-expression evidence for reaction...\n", + "1582\n", + "1582\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Len P: 687\n", + "num_removed 844\n", + "Len P AFTER 686\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 686\n", + "Reaction no. 334\n", + "Attempting to remove reaction: GLUVESSEC ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5084670000001097\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['FTHFLi', 'MTHFC', 'MTHFD'], inactive_NC:['GLUVESSEC']\n", + "Zero-expression evidence for reaction...\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "Len P: 686\n", + "num_removed 844\n", + "Len P AFTER 685\n", + "No reactions removed\n", + "result 1.0\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 685\n", + "Reaction no. 335\n", + "Attempting to remove reaction: GLUt6 ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 22 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5346459999996114\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 23 , inactive_C: ['GGH_6DHFe', 'CAATPS', 'GGH_10FTHF5GLUe', 'GGH_10FTHF6GLUe', 'CYSTGLUex', 'GGH_5THFe', 'GGH_6THFe', 'GGH_7THFe', 'NaKt', 'NDPK5m', 'GGH_5DHFe', 'GGH_7DHFe', 'GGH_10FTHF7GLUe'], inactive_NC:['EX_10fthf7glu_e', 'EX_10fthf_e', 'GLUVESSEC', 'NCKt', 'EX_7thf_e', 'EX_dhf_e', 'HKt', 'EX_7dhf_e', 'EX_thf_e', 'GLUt6']\n", + "Zero-expression evidence for reaction...\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "Len P: 685\n", + "num_removed 844\n", + "Len P AFTER 684\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 684\n", + "Reaction no. 336\n", + "Attempting to remove reaction: PNTOt5 ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4721039999999448\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['PPCDC', 'PNTK', 'DPCOAK', 'PPNCL3'], inactive_NC:['EX_pnto__R_e', 'PNTOt5']\n", + "Zero-expression evidence for reaction...\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "Len P: 684\n", + "num_removed 844\n", + "Len P AFTER 683\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 683\n", + "Reaction no. 337\n", + "Attempting to remove reaction: BTNt3i ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.327111000000059\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PUNP1', 'BTNt2i'], inactive_NC:['BTNt3i']\n", + "Zero-expression evidence for reaction...\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "Len P: 683\n", + "num_removed 844\n", + "Len P AFTER 682\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 682\n", + "Reaction no. 338\n", + "Attempting to remove reaction: CBPS ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3243539999998575\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['OMPDC', 'ORPT'], inactive_NC:['CBPS', 'DHORD9', 'ASPCT', 'DHORTS']\n", + "Zero-expression evidence for reaction...\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "Len P: 682\n", + "num_removed 844\n", + "Len P AFTER 681\n", + "No reactions removed\n", + "result 1.1\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 681\n", + "Reaction no. 339\n", + "Attempting to remove reaction: EX_fol_e ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2363620000000992\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['5MTHFt', 'FOLR2'], inactive_NC:['EX_5mthf_e', 'FOLt2', 'EX_fol_e']\n", + "Reaction EX_fol_e is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 680\n", + "Reaction no. 340\n", + "Attempting to remove reaction: EX_thmtp_e ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2815229999996518\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['HCO3_CLt', '5MTHFt', 'THMt3', 'FOLR2'], inactive_NC:['EX_thm_e', 'FOLt2', 'EX_thmtp_e', 'CLOHtex2', 'EX_5mthf_e', 'EX_fol_e', 'THMTPt']\n", + "Reaction EX_thmtp_e is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 679\n", + "Reaction no. 341\n", + "Attempting to remove reaction: EX_prostgd2_e ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2103919999999562\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['PGS', 'FTHFLi', 'MTHFC', 'MTHFD'], inactive_NC:['EX_prostgd2_e', 'PROSTGD2t', 'PGDI']\n", + "Reaction EX_prostgd2_e is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 678\n", + "Reaction no. 342\n", + "Attempting to remove reaction: EX_bilirub_e ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 677\n", + "Reaction no. 343\n", + "Attempting to remove reaction: SARCStm ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2472090000001117\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['FPGS8m', 'CREATt4_2_r', 'FPGS7m', 'MTHFCm', 'FPGS9m'], inactive_NC:['EX_creat_e', 'SARCStm', 'GLYAMDTRc', 'SARCStex', 'SARDHm', '10FTHF5GLUtm', 'EX_sarcs_e', '10FTHF7GLUtm', 'GACMTRc', '10FTHF6GLUtm']\n", + "Reaction SARCStm is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 676\n", + "Reaction no. 344\n", + "Attempting to remove reaction: EX_ncam_e ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5543189999998503\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['NDPK5m'], inactive_NC:['EX_ncam_e', 'EX_nadp_e', 'EX_adprbp_e', 'NADPNe']\n", + "Reaction EX_ncam_e is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 675\n", + "Reaction no. 345\n", + "Attempting to remove reaction: EBASTINEOHtr ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.484429000000091\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['FTHFLi', 'MTHFC', 'MTHFD'], inactive_NC:['EBASTINEte', 'EX_ebastineoh_e', 'P4504F123r', 'EBASTINEtr', 'EBASTINEOHtr', 'EBASTINEOHte', 'EX_ebastine_e']\n", + "Reaction EBASTINEOHtr is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 674\n", + "Reaction no. 346\n", + "Attempting to remove reaction: EBASTINEtr ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5060429999998632\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['FTHFLi', 'NKCC2t', 'MTHFC', 'MTHFD'], inactive_NC:['EBASTINEte', 'EX_ebastineoh_e', 'P4504F123r', 'EBASTINEtr', 'EBASTINEOHtr', 'EBASTINEOHte', 'EX_ebastine_e']\n", + "Reaction EBASTINEtr is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 673\n", + "Reaction no. 347\n", + "Attempting to remove reaction: HESTRATRIOLtr ...\n", + "Initial PM reactions: 1582\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2933579999998983\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['FTHFLi', 'MTHFD', 'HSD17B8r', 'LDH_L', 'HSD17B7r', 'MTHFC'], inactive_NC:['P4501B1r', 'HESTRATRIOLtr', 'EX_hestratriol_e', 'MALSO4tm', 'FUMSO4tm', 'ESTRONESt2', 'ESTRONEtr', 'HESTRATRIOLte', 'EX_estrones_e']\n", + "Reaction HESTRATRIOLtr is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 672\n", + "Reaction no. 348\n", + "Attempting to remove reaction: EX_o2_e ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 671\n", + "Reaction no. 349\n", + "Attempting to remove reaction: EX_o2s_e ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 85 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3729160000002594\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 86 , inactive_C: ['GCALDD', 'CATp', 'SPODM', 'FAOXC161802m', 'DUTPDPn', 'C161CPT22', 'FBA4', 'XAOx', 'ALAR', 'RNDR4', 'GLYCLTDy', 'DCSPTN1CPT1', 'PI345P3Pn', 'CAT2p', 'PYRt2p', 'PUNP7', 'DCSPTN1CPT2', 'C161CRN2t', 'C161CPT12', 'FAOXC2252053m', 'GLXO1', 'NTD10', 'FAOXC2251836m', 'XAO2x', 'SPODMx', 'XANDp', 'NDPK6n', 'SPODMn', 'DCSPTN1CRNt', 'DAGKn_hs'], inactive_NC:['PA_HStn', 'H2Otp', 'GLYCTO1p', 'ASCBOX', 'PMTCOAtx', 'GLXtp', 'ETOHtx', 'DESAT22_1p', 'EX_oxa_e', 'GUAD', 'DCSPTN1COAtx', 'URATEt', 'PI45P5Pn', 'DALAxt', 'ARTFR61', 'O2St', 'PIK4n', 'PI4P4Pn', 'H2O2tn', 'ADRNCOAtx', 'GLYCLTtp', 'DUDPtn', 'RTOT6', 'PI5P4Kn', 'PI34P4Pn', 'PI45P3Kn', 'DALAOXx', 'MI14Ptn', 'PIK3n', 'O2Stn', 'ACOAO7p', 'PI4P3Kn', 'HDD2COAtx', 'URATEtx', 'EX_o2s_e', 'PI4PLCn', 'PI3P3Pn', 'PI34P3Pn', 'DUMPtn', 'PI34P5Kn', 'HXANtx', 'O2tn', 'PAIL_HStn', 'PI345P5Pn', 'NH4tp', 'XANtx', 'O2Stx', 'ARTFR212', 'PI3P4Kn', 'MI1P_Dtn', 'EX_urate_e', 'KHK2', 'PIPLCn', 'ACALDtx', 'PI4P5Kn', 'PIK5n']\n", + "Reaction EX_o2s_e is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 670\n", + "Reaction no. 350\n", + "Attempting to remove reaction: CAROtr ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 13 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2614869999997609\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 14 , inactive_C: ['GLCt1', 'RDH2a', 'RDH1a'], inactive_NC:['RETFAt1', 'EX_retinol_9_cis_e', 'RETH1e', 'CAROtr', 'RETI1', 'RETH2e', 'EX_retinol_cis_11_e', 'EX_caro_e', 'RAI2', 'BCDO', 'RETFAt2']\n", + "Reaction CAROtr is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 669\n", + "Reaction no. 351\n", + "Attempting to remove reaction: EX_adprbp_e ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4735070000001542\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['PUNP1'], inactive_NC:['EX_ncam_e', 'EX_nadp_e', 'EX_adprbp_e', 'NADPNe']\n", + "Reaction EX_adprbp_e is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 844 (119 core, 725 non-core); Num. remaining: 668\n", + "Reaction no. 352\n", + "Attempting to remove reaction: EX_nadp_e ...\n", + "Initial PM reactions: 1582\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.440675999999712\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: [], inactive_NC:['EX_ncam_e', 'EX_nadp_e', 'EX_adprbp_e', 'NADPNe']\n", + "Reaction EX_nadp_e is not in Z\n", + "1582\n", + "1582\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1578\n", + "Num. removed: 848 (119 core, 729 non-core); Num. remaining: 667\n", + "Reaction no. 353\n", + "Attempting to remove reaction: EX_nrvnc_e ...\n", + "Initial PM reactions: 1578\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5124879999998484\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['CREATt4_2_r', 'FACOAL241'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'ARTFR45', 'MALSO4tm', 'FUMSO4tm', 'GACMTRc', 'EX_nrvnc_e', 'FATP9t']\n", + "Reaction EX_nrvnc_e is not in Z\n", + "1578\n", + "1578\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 848 (119 core, 729 non-core); Num. remaining: 666\n", + "Reaction no. 354\n", + "Attempting to remove reaction: EX_arachd_e ...\n", + "Initial PM reactions: 1578\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2778120000002673\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['FACOAL204_copy2', 'PGS'], inactive_NC:['EX_prostgd2_e', 'PROSTGD2t', 'EX_arachd_e', 'FATP5t', 'PGDI']\n", + "Reaction EX_arachd_e is not in Z\n", + "1578\n", + "1578\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 848 (119 core, 729 non-core); Num. remaining: 665\n", + "Reaction no. 355\n", + "Attempting to remove reaction: VITD3tm ...\n", + "Initial PM reactions: 1578\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1969919999996819\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['PUNP1'], inactive_NC:['VITD3tm']\n", + "Reaction VITD3tm is not in Z\n", + "1578\n", + "1578\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 848 (119 core, 729 non-core); Num. remaining: 664\n", + "Reaction no. 356\n", + "Attempting to remove reaction: VITD3tm3 ...\n", + "Initial PM reactions: 1578\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2750260000002527\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['24_25VITD3Hm'], inactive_NC:['24_25DHVITD3tm', 'VITD3tm3', 'EX_2425dhvitd3_e', '24_25DHVITD3t', 'VITD3tm', 'EX_vitd3_e', 'VITD3Hm']\n", + "Reaction VITD3tm3 is not in Z\n", + "1578\n", + "1578\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 848 (119 core, 729 non-core); Num. remaining: 663\n", + "Reaction no. 357\n", + "Attempting to remove reaction: LIMNENte ...\n", + "Initial PM reactions: 1578\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2799839999997857\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['LIMNENte', 'EX_perillyl_e', 'P4502C93', 'PERILLYLte', 'EX_limnen_e']\n", + "Reaction LIMNENte is not in Z\n", + "1578\n", + "1578\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1573\n", + "Num. removed: 853 (119 core, 734 non-core); Num. remaining: 659\n", + "Reaction no. 358\n", + "Attempting to remove reaction: NACASPtm ...\n", + "Initial PM reactions: 1573\n", + "check_model_function done ....\n", + "Num. removed: 853 (119 core, 734 non-core); Num. remaining: 658\n", + "Reaction no. 359\n", + "Attempting to remove reaction: AACTtm ...\n", + "Initial PM reactions: 1573\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.246483999999782\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['FTHFLi', 'MTHFC', 'MTHFD'], inactive_NC:['GLYATm', 'AOBUTDsm', 'AACTtm', 'AACTOOR']\n", + "Reaction AACTtm is not in Z\n", + "1573\n", + "1573\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 853 (119 core, 734 non-core); Num. remaining: 657\n", + "Reaction no. 360\n", + "Attempting to remove reaction: 5ADTSTSTERONESte ...\n", + "Initial PM reactions: 1573\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4792689999999311\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['CREATt4_2_r'], inactive_NC:['EX_5adtststerone_e', 'EX_creat_e', 'GLYAMDTRc', '5ADTSTSTERONEte', 'EX_5adtststerones_e', '5ADTSTSTERONESte', 'GACMTRc', '5ADTSTSTERONESULT']\n", + "Reaction 5ADTSTSTERONESte is not in Z\n", + "1573\n", + "1573\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 853 (119 core, 734 non-core); Num. remaining: 656\n", + "Reaction no. 361\n", + "Attempting to remove reaction: 5ADTSTSTERONEte ...\n", + "Initial PM reactions: 1573\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5255429999997432\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['EX_5adtststerone_e', 'EX_5adtststerones_e', '5ADTSTSTERONESte', '5ADTSTSTERONESULT', '5ADTSTSTERONEte']\n", + "Reaction 5ADTSTSTERONEte is not in Z\n", + "1573\n", + "1573\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1568\n", + "Num. removed: 858 (119 core, 739 non-core); Num. remaining: 653\n", + "Reaction no. 362\n", + "Attempting to remove reaction: SARCStex ...\n", + "Initial PM reactions: 1568\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4835170000001199\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['MTHFCm', 'FPGS8m', 'FPGS9m', 'FPGS7m'], inactive_NC:['SARCStm', 'SARCStex', 'SARDHm', '10FTHF5GLUtm', 'EX_sarcs_e', '10FTHF7GLUtm', '10FTHF6GLUtm']\n", + "Reaction SARCStex is not in Z\n", + "1568\n", + "1568\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 858 (119 core, 739 non-core); Num. remaining: 652\n", + "Reaction no. 363\n", + "Attempting to remove reaction: RETFAt ...\n", + "Initial PM reactions: 1568\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2696069999997235\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['SERtN1'], inactive_NC:['RETFAt', 'RETt', 'RETHe']\n", + "Reaction RETFAt is not in Z\n", + "1568\n", + "1568\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 858 (119 core, 739 non-core); Num. remaining: 651\n", + "Reaction no. 364\n", + "Attempting to remove reaction: 4MTOLBUTAMIDEte ...\n", + "Initial PM reactions: 1568\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2235529999998107\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['P4502C9', 'TOLBUTAMIDEte', '4MTOLBUTAMIDEte', 'EX_4mtolbutamide_e', 'EX_tolbutamide_e']\n", + "Reaction 4MTOLBUTAMIDEte is not in Z\n", + "1568\n", + "1568\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1563\n", + "Num. removed: 863 (119 core, 744 non-core); Num. remaining: 647\n", + "Reaction no. 365\n", + "Attempting to remove reaction: HTAXOLte ...\n", + "Initial PM reactions: 1563\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.252100000000155\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['GLCt1', 'CREATt4_2_r', 'SERtN1'], inactive_NC:['TAXOLte', 'EX_creat_e', 'GLYAMDTRc', 'HTAXOLte', 'P4502C8', 'GACMTRc', 'EX_taxol_e', 'EX_htaxol_e']\n", + "Reaction HTAXOLte is not in Z\n", + "1563\n", + "1563\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 863 (119 core, 744 non-core); Num. remaining: 646\n", + "Reaction no. 366\n", + "Attempting to remove reaction: TAXOLte ...\n", + "Initial PM reactions: 1563\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5055170000000544\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['PUNP1'], inactive_NC:['EX_pi_e', 'TAXOLte', 'HTAXOLte', 'P4502C8', 'EX_taxol_e', 'EX_htaxol_e']\n", + "Reaction TAXOLte is not in Z\n", + "1563\n", + "1563\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 863 (119 core, 744 non-core); Num. remaining: 645\n", + "Reaction no. 367\n", + "Attempting to remove reaction: EX_5htrp_e ...\n", + "Initial PM reactions: 1563\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.491269000000102\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['EX_5htrp_e', '5HTRPVESSEC', 'TRPHYDRO2']\n", + "Reaction EX_5htrp_e is not in Z\n", + "1563\n", + "1563\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1560\n", + "Num. removed: 866 (119 core, 747 non-core); Num. remaining: 643\n", + "Reaction no. 368\n", + "Attempting to remove reaction: EX_ala_B_e ...\n", + "Initial PM reactions: 1560\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 12 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.573591999999735\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 13 , inactive_C: ['DHPM1', 'CREATt4_2_r', 'PYNP2r', 'BAMPPALDOX'], inactive_NC:['EX_creat_e', 'EX_ala_B_e', 'GLYAMDTRc', '13DAMPPOX', 'BALAVECSEC', 'SPMDOX', 'UPPN', 'GACMTRc', 'DURAD']\n", + "Reaction EX_ala_B_e is not in Z\n", + "1560\n", + "1560\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 866 (119 core, 747 non-core); Num. remaining: 642\n", + "Reaction no. 369\n", + "Attempting to remove reaction: EX_ps_hs_e ...\n", + "Initial PM reactions: 1560\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2423969999999827\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['PSFLIP', 'EX_ps_hs_e']\n", + "Reaction EX_ps_hs_e is not in Z\n", + "1560\n", + "1560\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1558\n", + "Num. removed: 868 (119 core, 749 non-core); Num. remaining: 641\n", + "Reaction no. 370\n", + "Attempting to remove reaction: EX_pe_hs_e ...\n", + "Initial PM reactions: 1558\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 29 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2939149999997426\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 30 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'DCYTD', 'RNDR4'], inactive_NC:['THMDt4', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'PEFLIP', 'NDP6', 'AHCYStr']\n", + "Reaction EX_pe_hs_e is not in Z\n", + "1558\n", + "1558\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 868 (119 core, 749 non-core); Num. remaining: 640\n", + "Reaction no. 371\n", + "Attempting to remove reaction: EX_pnto__R_e ...\n", + "Initial PM reactions: 1558\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2670090000001437\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['DPCOAK', 'PPNCL3', 'PNTK', 'GLUt2m', 'PPCDC'], inactive_NC:['PNTOt5', 'EX_pnto__R_e', 'EX_gly_e']\n", + "Reaction EX_pnto__R_e is not in Z\n", + "1558\n", + "1558\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 868 (119 core, 749 non-core); Num. remaining: 639\n", + "Reaction no. 372\n", + "Attempting to remove reaction: DM_13_cis_oretn_n ...\n", + "Initial PM reactions: 1558\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5335650000001806\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['ENO', 'PGM'], inactive_NC:['DM_13_cis_oretn_n', 'ORETNtn2', 'ORETNF2']\n", + "Reaction DM_13_cis_oretn_n is not in Z\n", + "1558\n", + "1558\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 868 (119 core, 749 non-core); Num. remaining: 638\n", + "Reaction no. 373\n", + "Attempting to remove reaction: DM_13_cis_retn_n ...\n", + "Initial PM reactions: 1558\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4732090000002245\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['RAtn3', 'DM_13_cis_retn_n', 'EX_pi_e']\n", + "Reaction DM_13_cis_retn_n is not in Z\n", + "1558\n", + "1558\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 868 (119 core, 749 non-core); Num. remaining: 637\n", + "Reaction no. 374\n", + "Attempting to remove reaction: DM_avite1_c ...\n", + "Initial PM reactions: 1558\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4635560000001533\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['AVITE1t', 'DM_avite1_c', 'EX_avite1_e']\n", + "Reaction DM_avite1_c is not in Z\n", + "1558\n", + "1558\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1555\n", + "Num. removed: 871 (119 core, 752 non-core); Num. remaining: 634\n", + "Reaction no. 375\n", + "Attempting to remove reaction: DM_avite2_c ...\n", + "Initial PM reactions: 1555\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2533950000001823\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['FTHFLi', 'MTHFC', 'MTHFD'], inactive_NC:['DM_avite2_c', 'AVITE2t', 'EX_avite2_e', 'MALSO4tm', 'FUMSO4tm']\n", + "Reaction DM_avite2_c is not in Z\n", + "1555\n", + "1555\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 871 (119 core, 752 non-core); Num. remaining: 633\n", + "Reaction no. 376\n", + "Attempting to remove reaction: DM_bvite_c ...\n", + "Initial PM reactions: 1555\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2298609999998007\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['NDPK5m'], inactive_NC:['DM_bvite_c', 'BVITEt', 'EX_bvite_e']\n", + "Reaction DM_bvite_c is not in Z\n", + "1555\n", + "1555\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 871 (119 core, 752 non-core); Num. remaining: 632\n", + "Reaction no. 377\n", + "Attempting to remove reaction: DM_hretn_n ...\n", + "Initial PM reactions: 1555\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2225350000003345\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['CREATt4_2_r', 'SERtN1'], inactive_NC:['GLYAMDTRc', 'EX_creat_e', 'RAHY', 'DM_hretn_n', 'GACMTRc', 'HRETNtn']\n", + "Reaction DM_hretn_n is not in Z\n", + "1555\n", + "1555\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 871 (119 core, 752 non-core); Num. remaining: 631\n", + "Reaction no. 378\n", + "Attempting to remove reaction: DM_kdn_c ...\n", + "Initial PM reactions: 1555\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 65 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6195889999999054\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 66 , inactive_C: ['UDPDOLPT_U', 'GLDBRAN', 'AHEXASE2ly', 'GGNG', 'GBA', 'GALKr', 'UDPDOLPT_L', 'GLGNS1', 'NACHEX27ly', 'UGCG', 'GLCURtly', 'CERT1rt', 'GLCAASE8ly', 'GLPASE2', 'GASNASEly', 'GLBRAN', 'GLPASE1', 'UGLT', 'GASNASE2ly', 'UDPGD', 'HEX4', 'A_MANASEly', 'GLCAASE9ly', 'FUCASEe', 'ACNAM9PL2', 'SIAASEly', 'GALASE1ly', 'GALUi', 'CERT2rt', 'AHEXASEly', 'ACNAMlt'], inactive_NC:['EX_n2m2nmasn_e', 'MANtly', 'DOLPH_Ler', 'ENGASEly', 'DM_kdn_c', 'HAS2', 'DOLGPP_Uer', 'DOLGLCP_Uter', 'DOLP_Uter', 'NDP7er', 'KDNH', 'DOLICHOL_Uter', 'HAtly', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GUR1PP', 'UDPG4E', 'ENGASE2ly', 'GALtly', 'DOLP_Lter', 'UDPG1P', 'DOLK_U', 'EX_s2l2fn2m2masn_e', 'N2M2NMASNtly', 'DOLGLCP_Lter', 'ATPasel', 'B_MANNASEly', 'UDPGLCter', 'UDPGNP', 'DOLPH_Uer', 'DOLK_L', 'ACGAMtly', 'HAS1', 'DM_Asn_X_Ser_Thr_l']\n", + "Reaction DM_kdn_c is not in Z\n", + "1555\n", + "1555\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 871 (119 core, 752 non-core); Num. remaining: 630\n", + "Reaction no. 379\n", + "Attempting to remove reaction: DM_oretn_n ...\n", + "Initial PM reactions: 1555\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5056799999997565\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: [], inactive_NC:['EX_gly_e', 'CYTK1', 'GLYt2r', 'DM_oretn_n', 'ORETNtn', 'ORETNF']\n", + "Reaction DM_oretn_n is not in Z\n", + "1555\n", + "1555\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1549\n", + "Num. removed: 877 (119 core, 758 non-core); Num. remaining: 626\n", + "Reaction no. 380\n", + "Attempting to remove reaction: DM_yvite_c ...\n", + "Initial PM reactions: 1549\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4773869999999079\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['NKCC2t', 'LEUTAm'], inactive_NC:['DM_yvite_c', 'MALSO4tm', 'LEUt5m', 'FUMSO4tm', 'YVITEt', 'EX_yvite_e']\n", + "Reaction DM_yvite_c is not in Z\n", + "1549\n", + "1549\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 877 (119 core, 758 non-core); Num. remaining: 625\n", + "Reaction no. 381\n", + "Attempting to remove reaction: DOLGLCP_Lter ...\n", + "Initial PM reactions: 1549\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1855749999999716\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['UDPDOLPT_L'], inactive_NC:['DOLPH_Ler', 'DOLK_L', 'DOLGLCP_Lter', 'DOLICHOL_Lter', 'DOLGPP_Ler', 'DOLP_Lter']\n", + "Reaction DOLGLCP_Lter is not in Z\n", + "1549\n", + "1549\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 877 (119 core, 758 non-core); Num. remaining: 624\n", + "Reaction no. 382\n", + "Attempting to remove reaction: DOLGLCP_Uter ...\n", + "Initial PM reactions: 1549\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2157210000000305\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['UDPDOLPT_U'], inactive_NC:['DOLICHOL_Uter', 'DOLK_U', 'DOLPH_Uer', 'DOLGPP_Uer', 'DOLGLCP_Uter', 'DOLP_Uter']\n", + "Reaction DOLGLCP_Uter is not in Z\n", + "1549\n", + "1549\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 877 (119 core, 758 non-core); Num. remaining: 623\n", + "Reaction no. 383\n", + "Attempting to remove reaction: DOLICHOL_Lter ...\n", + "Initial PM reactions: 1549\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2536059999997633\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['DOLICHOL_Lter', 'MALSO4tm', 'DOLPH_Ler', 'FUMSO4tm', 'DOLK_L']\n", + "Reaction DOLICHOL_Lter is not in Z\n", + "1549\n", + "1549\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 877 (119 core, 758 non-core); Num. remaining: 622\n", + "Reaction no. 384\n", + "Attempting to remove reaction: DOLICHOL_Uter ...\n", + "Initial PM reactions: 1549\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1881969999999455\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['DOLICHOL_Uter', 'DOLPH_Uer', 'DOLK_U']\n", + "Reaction DOLICHOL_Uter is not in Z\n", + "1549\n", + "1549\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1546\n", + "Num. removed: 880 (119 core, 761 non-core); Num. remaining: 619\n", + "Reaction no. 385\n", + "Attempting to remove reaction: EX_2425dhvitd2_e ...\n", + "Initial PM reactions: 1546\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5114369999996597\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['SERtN1', 'NKCC2t', '24_25VITD2Hm'], inactive_NC:['EX_pi_e', 'EX_25hvitd2_e', '24_25DHVITD2tm', '24_25DHVITD2t', 'EX_2425dhvitd2_e']\n", + "Reaction EX_2425dhvitd2_e is not in Z\n", + "1546\n", + "1546\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 880 (119 core, 761 non-core); Num. remaining: 618\n", + "Reaction no. 386\n", + "Attempting to remove reaction: EX_2425dhvitd3_e ...\n", + "Initial PM reactions: 1546\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4884220000003552\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['24_25VITD3Hm', 'PUNP1'], inactive_NC:['24_25DHVITD3tm', 'EX_2425dhvitd3_e', '24_25DHVITD3t', 'EX_vitd3_e', 'VITD3Hm']\n", + "Reaction EX_2425dhvitd3_e is not in Z\n", + "1546\n", + "1546\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 880 (119 core, 761 non-core); Num. remaining: 617\n", + "Reaction no. 387\n", + "Attempting to remove reaction: EX_24nph_e ...\n", + "Initial PM reactions: 1546\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.249663000000055\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['EX_24nph_e', 'P4502E1', '24NPHte']\n", + "Reaction EX_24nph_e is not in Z\n", + "1546\n", + "1546\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1543\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 614\n", + "Reaction no. 388\n", + "Attempting to remove reaction: EX_25hvitd2_e ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2267809999998462\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['24_25VITD2Hm', 'LEUTAm'], inactive_NC:['EX_25hvitd2_e', 'LEUt5m', '24_25DHVITD2tm', '24_25DHVITD2t', 'EX_2425dhvitd2_e']\n", + "Reaction EX_25hvitd2_e is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 613\n", + "Reaction no. 389\n", + "Attempting to remove reaction: EX_2mcit_e ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2918250000002445\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['ACS2', 'ACITL', 'ACCOAL'], inactive_NC:['2MCITt', 'OBDHc', 'EX_2mcit_e', 'MCITS']\n", + "Reaction EX_2mcit_e is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 612\n", + "Reaction no. 390\n", + "Attempting to remove reaction: EX_34dhoxpeg_e ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4697799999999006\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['34DHOXPEGOX', '41R1H2MAE12BOOX', 'SFGTHi', '41R2A1H12BOOX', 'FALDH'], inactive_NC:['MAOX', '34DHOXPEGt', 'EX_34dhoxpeg_e']\n", + "Reaction EX_34dhoxpeg_e is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 611\n", + "Reaction no. 391\n", + "Attempting to remove reaction: EX_3aib_e ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5103320000002896\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['SERtN1'], inactive_NC:['3AIBTm', 'EX_3aib_e', '3AIBt', '3AIBtm']\n", + "Reaction EX_3aib_e is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 610\n", + "Reaction no. 392\n", + "Attempting to remove reaction: EX_4hphac_e ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2056910000001153\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['TYROXDAc', '4HOXPACDOX_NADP'], inactive_NC:['EX_pi_e', 'EX_4hphac_e', 'HPACtr']\n", + "Reaction EX_4hphac_e is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 609\n", + "Reaction no. 393\n", + "Attempting to remove reaction: EX_4nph_e ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2257810000000973\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['4NPHSULT'], inactive_NC:['EX_4nph_e', '4NPHSFte', '4NPHte', 'EX_4nphsf_e']\n", + "Reaction EX_4nph_e is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 608\n", + "Reaction no. 394\n", + "Attempting to remove reaction: DOLP_Lter ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4451679999997395\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['MALSO4tm', 'FUMSO4tm', 'DOLP_Lter']\n", + "Reaction DOLP_Lter is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 607\n", + "Reaction no. 395\n", + "Attempting to remove reaction: DOLP_Uter ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5212000000001353\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['UDPDOLPT_U', 'SERtN1', 'PUNP1'], inactive_NC:['DOLGLCP_Uter', 'DOLP_Uter', 'DOLGPP_Uer']\n", + "Reaction DOLP_Uter is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 606\n", + "Reaction no. 396\n", + "Attempting to remove reaction: EX_4nphsf_e ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4693329999995512\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['4NPHSULT'], inactive_NC:['EX_4nph_e', '4NPHSFte', '4NPHte', 'EX_4nphsf_e']\n", + "Reaction EX_4nphsf_e is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 605\n", + "Reaction no. 397\n", + "Attempting to remove reaction: EX_4pyrdx_e ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2516709999999875\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['PYDXDH'], inactive_NC:['EX_4pyrdx_e', 'EX_pydx_e', 'PYDXtr', '4PYRDX']\n", + "Reaction EX_4pyrdx_e is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 604\n", + "Reaction no. 398\n", + "Attempting to remove reaction: EX_abt_e ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.21955300000036\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['NDPK5m', 'ARABR'], inactive_NC:['ARAB_Lt', 'ABTt', 'EX_arab__L_e', 'EX_abt_e']\n", + "Reaction EX_abt_e is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 883 (119 core, 764 non-core); Num. remaining: 603\n", + "Reaction no. 399\n", + "Attempting to remove reaction: EX_acald_e ...\n", + "Initial PM reactions: 1543\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2573959999999715\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['ACALDt', 'EX_acald_e', 'MALtm']\n", + "Reaction EX_acald_e is not in Z\n", + "1543\n", + "1543\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1540\n", + "Num. removed: 886 (119 core, 767 non-core); Num. remaining: 600\n", + "Reaction no. 400\n", + "Attempting to remove reaction: EX_caro_e ...\n", + "Initial PM reactions: 1540\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4915079999996124\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['RDH2a', 'RDH1a', 'PUNP5'], inactive_NC:['RETFAt1', 'EX_pi_e', 'EX_retinol_9_cis_e', 'RETH1e', 'CAROtr', 'RETI1', 'RETH2e', 'EX_retinol_cis_11_e', 'EX_caro_e', 'RAI2', 'BCDO', 'RETFAt2']\n", + "Reaction EX_caro_e is not in Z\n", + "1540\n", + "1540\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 886 (119 core, 767 non-core); Num. remaining: 599\n", + "Reaction no. 401\n", + "Attempting to remove reaction: EX_coumarin_e ...\n", + "Initial PM reactions: 1540\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5350359999997636\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['P4502A6'], inactive_NC:['EX_pi_e', 'EX_coumarin_e', 'COUMARINte', 'HCOUMARINte', 'EX_hcoumarin_e']\n", + "Reaction EX_coumarin_e is not in Z\n", + "1540\n", + "1540\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 886 (119 core, 767 non-core); Num. remaining: 598\n", + "Reaction no. 402\n", + "Attempting to remove reaction: EX_crmp_hs_e ...\n", + "Initial PM reactions: 1540\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.238803000000189\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['CERK'], inactive_NC:['EX_crmp_hs_e', 'CRMPte']\n", + "Reaction EX_crmp_hs_e is not in Z\n", + "1540\n", + "1540\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 886 (119 core, 767 non-core); Num. remaining: 597\n", + "Reaction no. 403\n", + "Attempting to remove reaction: EX_cyan_e ...\n", + "Initial PM reactions: 1540\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2007920000000922\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['MCPST'], inactive_NC:['TCYNTt', 'EX_tcynt_e', 'EX_cyan_e', 'CYANt']\n", + "Reaction EX_cyan_e is not in Z\n", + "1540\n", + "1540\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 886 (119 core, 767 non-core); Num. remaining: 596\n", + "Reaction no. 404\n", + "Attempting to remove reaction: EX_dopasf_e ...\n", + "Initial PM reactions: 1540\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.487691000000268\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['DOPASULT'], inactive_NC:['DOPASFt', 'EX_dopasf_e']\n", + "Reaction EX_dopasf_e is not in Z\n", + "1540\n", + "1540\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 886 (119 core, 767 non-core); Num. remaining: 595\n", + "Reaction no. 405\n", + "Attempting to remove reaction: EX_avite2_e ...\n", + "Initial PM reactions: 1540\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4552330000001348\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['DM_avite2_c', 'EX_avite2_e', 'AVITE2t']\n", + "Reaction EX_avite2_e is not in Z\n", + "1540\n", + "1540\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1537\n", + "Num. removed: 889 (119 core, 770 non-core); Num. remaining: 593\n", + "Reaction no. 406\n", + "Attempting to remove reaction: EX_bhb_e ...\n", + "Initial PM reactions: 1537\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1154 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 3.9935780000000705\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1155 , inactive_C: ['C3STDH1Pr', 'CAMPt', 'PETOHMr_hs', 'FPGS7', 'GDHm', 'FAS160COA', 'MI145PK', 'AHCi', 'HPDCACRNt', 'GPAM_hs', 'C161CPT1', 'PI45P5P', 'GLUNm', 'ADRNCPT2', 'MTHFD', 'SQLSr', 'PRFGS', 'GGH_5THFl', 'FMNAT', 'LCYSTAT', 'PCHOLP_hs', 'CBPSam', 'FAOXC204184m', 'GLCAASE9ly', 'NTD2', 'PTDCACRNCPT2', 'GLNS', 'GGH_10FTHF6GLUe', 'XAO2x', 'LNLNCGCPT1', 'ACNAM9PL', 'TTDCPT1', 'FPGS9m', 'CITtbm', 'CYTDK1', 'PEPCKm', 'PGI', 'COAtim', 'MACACI', 'EICOSTETCPT2', 'HOXG', 'PPNCL3', 'DADA', 'FAEL204', 'G6Pter', 'RPI', 'PSP_L', 'CAT2p', 'GF6PTA', 'PI5P4K', 'DCSPTN1CPT2', 'PPA', 'UGLT', 'FATP2t', 'LPASE', 'GGH_5DHFe', 'LNS14DMr', 'RDH1a', 'CTPS2', 'SIAASEly', 'LNELDCCPT1', 'DADAe', 'FAOXC183803m', 'VACCCPT1', 'FAS120COA', 'HMBS', 'HSD17B7r', 'FAOXC2051843m', 'PFK26', 'CHLPCTD', 'ADNK1', 'GGH_7DHFl', 'FACOAL170', 'DESAT24_1', 'CATm', 'FPGSm', 'CYTD', 'PTDCACRNCPT1', 'FATP3t', 'DHCR241r', 'THYMDt1', 'ACITL', 'ORPT', 'RTOTAL2CRNCPT1', 'DLNLCGCPT1', 'FPGS3m', 'FPGS7m', 'LSTO2r', 'FAEL183', 'ACACT1r_copy1', 'FPGS2m', 'MEVK1x', 'A_MANASEly', 'IMPC', 'DESAT18_8', 'PYRt2m', 'TMDPK', '4NPHSULT', 'GLXO1', 'NTD10', 'STRDNCCRNt', 'MI34PP', 'MTAP', 'LNLNCGCPT2', 'PTPATi', 'ALCD2y', 'NTD5', 'DESAT18_4', 'XANDp', 'NDP3ex', 'IMPD', 'FAS80COA_L', 'ACNAMlt', 'MI134PP', 'VALTAim', 'FACOAL1832', 'C3STDH1r', 'DESAT18_9', 'ADNtm', 'GGNG', 'PNTK', 'HSD17B8r', 'PI45P3K', 'BUTt2m', 'GTHS', 'C160CRNt', 'GLGNS1', 'FPGS6', 'FAOXC183806m', 'G6PDH2r', 'DESAT18_6', 'MMMm', 'C161CRNt', 'ACYP', 'FPGS5', 'CPPPGO', 'GGH_6DHFl', 'ECOAH9m', 'ARGNm', 'FAOXC150m', 'BILIRED', 'HSD17B9r', 'PI4PLC', 'CSm', 'G6PDA', 'ORNDC', 'DHCRD1', 'PI3P5K', 'STRDNCCPT1', 'ICDHyr', 'STS4', 'MCLORi', 'FPGS8', 'PI35P3P', 'LYSt4', 'PNP', 'PRGNLONESULT', 'ADPRDP', 'NTP3e', 'EICOSTETCRNt', 'ELAIDCPT1', 'HISt4', 'MI145PP', 'HACD1m', 'KAS8', 'METLEUex', 'ESTSULT', 'FUCASEe', 'ALDD19x_P', 'GMPR', 'RTOTALCRNCPT1', 'SOAT12', 'ARGSS', 'CGLYt3_2', 'GGH_10FTHF6GLUl', 'GALUi', 'ACOAD1fm', 'TKT1', 'ADK1', 'ACOAD9m', 'NDPK6n', 'SERPT', 'GTHOm', 'AMPDA', 'DURIK1', 'C161CPT22', 'C161CPT2', 'SMS', 'GRTTx', 'PGPPT', 'TYMSULT', 'XAOx', '24_25VITD2Hm', 'PSERT', 'STS3', 'PI345P5P', 'C181CRNt', 'GLUt2m', 'NTD2e', 'ACACT1m', 'GGH_10FTHF7GLUl', 'GGH_7DHFe', 'OIVD3m', 'METS', 'METAT', 'ACETONEt2m', 'PI345P3P', 'FAOXC1811602m', 'PFK', 'SBPP3er', 'DGNSKm', 'C14STRr', 'FAOXC160', 'DESAT20_2', 'DHPM1', 'RTOTALCRNt', 'LSTO1r', 'XYLUR', 'CDS', 'RTOTAL3CRNCPT1', 'ALASm', 'CRNtim', 'OMPDC', 'ADNCYC', 'DUTPDPn', 'ASNS1', 'LEUTAm', 'PRAGSr', 'AHEXASE2ly', 'FUMAC', 'PUNP6', 'PMEVKx', 'UDPDOLPT_L', 'GGH_6DHFe', 'NTD1', 'PIPLC', '41R1H2MAE12BOOX', 'PI34P5K', 'FAOXC180', 'NTD4', 'MI1345PP', 'GGH_5THFe', 'PIK5', 'URIK1', 'PYNP2r', 'NT5C', 'SQLEr', 'OIVD2m', 'FAOXC2251836m', 'FPGS8m', 'ORNt', 'SFGTHi', 'NTD7', 'AHEXASEly', 'HEX10', 'ACOAD10m', 'HEX1', 'NTD9e', 'FOLR2', 'UGCG', 'PLA2_2', 'NTD8', 'LPS3', 'NDPK8', 'PUNP3', 'DMATTx', 'CYSTS', 'CAATPS', 'LEUt4', 'DHFR', 'GLCAASE8ly', 'FAS140COA', 'PETHCT', 'ASPTAm', 'GASNASEly', 'SUCOAS1m', 'RTOTALCRNCPT2', 'PRASCSi', 'ACS', 'TRPt4', 'HEX7', 'FAOXC2031836m', 'ETHAK', 'UAGDP', 'GGH_6THFl', 'SPODMm', 'PDHm', 'GCALDD', 'ABUTD', 'GMPS2', 'PUNP1', 'ACCOAC', 'PTDCACRNt', 'ECOAH1m', '3SALAASPm', 'NACHEX27ly', 'TMNDNCCRNt', 'TTDCRNt', 'RNDR3', 'PRPPS', 'PIK4', 'TYRTA', 'GGH_7THFl', 'PPPGOm', 'EICOSTETCPT1', 'SULFOX', 'DPGM', 'MI3PP', 'FPGS4', 'DGAT', 'AMANK', 'ACGAMK', 'MI4PP', 'FAOXC18280m', 'ACNAM9PL2', 'AGPAT1', 'TMNDNCCPT2', 'MGCHrm', 'FAOXC170m', 'FAOXC18480m', 'DHCR71r', 'NTD9', 'LNSTLSr', 'GK1', 'ACONT', 'PDE1', 'ECOAH12m', 'NDPK7', 'BUTt2r', 'DCSPTN1CPT1', 'THMt3', 'FPGS5m', 'GGH_10FTHF7GLUe', 'GLCURtly', 'DPCOAK', 'FACOAL161', 'TMDS', 'GLBRAN', 'LYSt5r', 'C181CPT1', 'FACOAL260', 'FACOAL245_1', 'GASNASE2ly', 'PIK3', 'C161CRN2t', 'FAOXC1811603m', '3SALATAim', 'NTD6', 'PGCD', 'GALASE1ly', 'CERT2rt', 'FPGS6m', 'FACOAL1821', 'PEAMNO', 'ME2', 'PROt4', 'VACCCPT2', 'GAMt1r', 'PAFH', 'SALMCOM2', 'GBA', 'AIRCr', 'ACGAM6PS', 'AICART', 'STRDNCCPT2', 'ALDD2x', 'C204CPT1', 'FACOAL181', 'FACOAL241', 'FBP26', 'ACRNtm', 'LNELDCCPT2', 'C180CRNt', 'NDPK1', 'C4STMO2Pr', 'C204CPT2', 'FAOXC16180m', 'LNLNCGCRNt', 'GLPASE1', 'MI1PP', 'HEX4', 'FAOXC182806m', 'C161CPT12', 'SBPP1er', 'UREAt', 'RBFK', 'IPDDIx', 'DPMVDx', 'TMNDNCCPT1', 'SLDx', 'RTOTAL3CRNt', 'PI4P5K', 'UDPDOLPT_U', 'LNLCCPT2', 'FTHFLi', 'LNELDCCRNt', 'GGH_5DHFl', 'OCOAT1m', 'LNLNCACPT2', 'HMGCOARx', 'FPGS4m', 'ILEt4', 'PSSA2_hs', 'ACS2', 'FACOAL180', 'UPP3S', 'CHOLK', 'ADRNCRNt', 'PYDXDH', 'CYSTA', 'PUNP7', 'DESAT18_3', 'CTPS1', 'FPGS2', 'LNLCCPT1', 'NTD4e', 'FACOAL150', 'DESAT18_5', 'FAOXC80', 'CDIPTr', 'C160CPT1', 'DHCR243r', 'ARGSL', 'FAOXC204', '24_25VITD3Hm', 'PI45PLC', 'MI14PP', 'FALDH', 'NDPK2', 'AMPTASECG', 'FAS100COA', 'GGH_10FTHF5GLUe', 'DLNLCGCRNt', 'EBP2r', 'C160CPT2', 'EBP1r', 'ADSL1r', 'FACOAL204_copy2', 'NTD11', 'SUCD1m', 'GGH_6THFe', 'PPCDC', 'SOAT11', 'ADMDC', 'OIVD1m', 'VALt4', 'CERK', 'ALDD2xm', 'ALDD2y', 'FACOAL244_1', 'CERT1rt', 'RTOTAL2CRNCPT2', 'FACOAL80', 'BTNt2i', 'C4STMO2r', 'GUACYC', 'MTHFCm', 'ETF', 'FAOXC2252053m', 'C180CPT2', 'CGMPt', 'ADRNCPT1', 'TALA', 'GTHPm', 'SPODMn', 'MCPST', 'CITtam', 'METt4', 'BAMPPALDOX', 'FAOXC161802m', 'CHSTEROLSULT', 'CYSTGLUex', 'DLNLCGCPT2', 'NMNATn', 'HIBDm', 'SADT', 'C4STMO1r', 'RNDR4', 'TKT2', 'PROSTGE1t3', 'GARFT', 'ALDD19xr', 'FAS180COA', 'FPGS9', 'UPPDC1', 'RTOTAL2CRNt', 'FACOAL140', 'AACOAT', 'NDP7ex', '5MTHFt', 'FAOXC2242046m', 'PI4P3K', 'SPRMS', 'GLPASE2', 'PRAIS', 'NaKt', 'UAG2EMA', 'UDPGD', 'HMGCOAS', '3DSPHR', 'ACCOAL', 'AMPTASECGe', 'RNDR1', 'ADSL2r', 'DCSPTN1CRNt', 'DESAT18_10', 'ARGt4', 'FAOXC140', 'DPGase', 'FAEL184', 'VACCCRNt', 'NNATn', 'DCYTD', 'MTHFC', 'STS2', 'GLUPRT', 'THMTP', 'FPGS3', 'ALCD2x', 'PUNP5', 'HMGLm', 'MMEm', 'CREATt4_2_r', 'PI3PP', 'PROSTGE2t3', 'FAOXC16080m', 'H2CO3D', 'PI345P3Pn', 'HACD9m', 'DHCR72r', 'FACOAL160', 'ADSS', 'ACGAMPM', 'TMDK1', 'NTD3', 'ELAIDCRNt', 'DAGKn_hs', 'HPDCACRNCPT1', 'ADPT', 'STS1', 'GLDBRAN', 'RTOTAL3CRNCPT2', 'DGK1', 'NDP8ex', 'FBA4', 'GGH_7THFe', 'FAEL205', 'GALKr', 'ARGLYSex', 'FAOXC1811601m', 'DOPASULT', 'HPDCACRNCPT2', 'SPMS', 'GGH_10FTHF5GLUl', 'TTDCPT2', 'DESAT20_1', 'LNLNCACRNt', 'PI3P4K', 'FACOAL245_2', 'FPGS', 'PI5P3K', 'ADSK', 'DHCR242r', 'DHCRD2', 'LNLCCRNt', 'RNDR2', 'DESAT18_7', '3SALATAi', 'ADK1m', 'C180CPT1', 'LNLNCACPT1', 'C181CPT2', 'ELAIDCPT2', 'RDH2a', 'ARGt5r'], inactive_NC:['24_25DHVITD3t', '7DHFtm', 'P4501B1r', 'EX_hestratriol_e', 'PCHOLPr_hs', 'MI14Ptn', 'EX_caro_e', 'DNDPt7m', 'H2Otn', 'GLCURter', 'L_LACDcm', 'PI3P3Pn', 'THMP', 'EX_25hvitd2_e', 'NICRNTtn', 'EX_gtp_e', 'DGK2m', 'FACOAL40im', 'PEFLIP', 'EX_but_e', 'PI345P5Pn', 'DNDPt53m', '10FTHFtl', 'ARTPLM2m', 'UNK3', 'DNDPt57m', 'VITD3Hm', 'EX_nrpphrsf_e', 'ACGAM2E', 'OBDHc', 'DNDPt20m', '7DHFtl', 'CYOR_u10m', 'CYSO', 'DM_dctp_m', 'LEUTA', 'LNLCt', 'ACP1_FMN', 'BALAVECSEC', 'EX_pnto__R_e', 'HSD3A1r', 'BHBt', 'ARTFR52', 'GULN3D', 'PROSTGE2t', 'NADN', 'EX_nrvnc_e', 'GALtly', 'PPAtr', 'HMGCOAtx', 'TCHOLAt3', 'P4504F123r', 'SARCStex', 'O2tm', 'EX_dad_2_e', 'FTHFDH', 'B_MANNASEly', 'CYANt', 'EX_2mcit_e', 'HESTRATRIOLte', 'PPAP', 'ACACT10m', 'ASNNm', 'DOLK_L', 'DNDPt12m', 'EX_fol_e', '2HCO3_NAt', 'EX_utp_e', 'PI4P5Kn', 'EX_mercplaccys_e', 'EX_ttdca_e', 'OCBTm', 'DNDPt56m', 'EX_tetpent3_e', 'PA_HSter', 'AKGDm', 'COt', 'TTDCAtr', 'EX_for_e', 'RETFAt2', 'PIK4n', 'EX_gam_e', 'GUR1PP', 'DNADDP', 'DNADtn', 'DNDPt58m', 'EX_10fthf7glu_e', 'OCCOAtm', 'URATEtx', 'ASPCT', 'MEOHtly', 'ARTFR208', 'FADDP', 'DNDPt52m', 'NMNAT', 'OCTAt', 'LRAT', 'ARTFR56', 'DNDPt43m', 'DM_sprm_c', 'DRPA', 'ARTFR206', 'EX_pro__L_e', 'PHACCOAGLNAC', 'RTOT_3', 'DADNt4', 'EX_hexc_e', 'EX_n2m2nmasn_e', 'NRPPHRSULT', 'NADPtru', 'LPS2', 'HAS2', '10FTHF6GLUtl', 'ARTFR55', 'EX_dhf_e', 'MALSO4tm', 'EX_lnlc_e', '5THFtm', 'EX_ppa_e', 'GLUt7l', 'EX_thymd_e', 'EX_pydx_e', 'MCCCrm', 'S2L2N2M2MASNtly', 'GCHOLAt3', 'ACCOALm', 'TYMSFt', 'ARTFR31', 'FADtru', 'XYLK', 'G6PPer', 'CAROtr', 'RETFAt', 'PYDXtr', 'DADNK', '24_25DHVITD3tm', 'SPHGNtr', 'DM_dgtp_m', 'UNK2', 'BPNT', 'ACGAMtly', 'ACNAMPH', 'FALDtly', '2DR1PP', 'ENGASEly', 'PPAer', 'EX_xoltri25_e', 'CYSGLTH', 'RETH1e', 'PIter', 'MAOX', 'ETOHMO', 'H2O2tn', 'ARTFR46', 'UPPN', 'EX_octa_e', 'AACTtm', 'FOLt2', 'GHMT2r', 'DNDPt13m', 'PI34P3Pn', 'HPDCAt', 'MI14P4P', 'SLDt', 'RETt', 'PHEMEtm', 'GULNter', 'DNDPt21m', 'UDPGLCter', 'PPItx', 'HISTAVESSEC', 'HSD3B2r', 'EX_3aib_e', 'EX_xolest_hs_e', 'DM_datp_n', 'ETHP', 'XOLESTte', 'CO2tp', 'BILIRUBt2', 'EX_hpdca_e', 'MANtly', 'DM_kdn_c', 'EX_pheacgln_e', 'CHOLATEt3', 'EX_camp_e', 'EX_estrones_e', 'EX_val__L_e', 'ACALDtm', 'EX_tetpent6_e', 'C204CRNt', '3SPYRSPm', 'DNDPt30m', 'NADHtru', 'PTRCOX1', 'TETTET6t', 'ACOAH', 'RETFAt1', 'EX_35cgmp_e', 'CYTDt5', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'PAIL_HStn', 'ESTRONEtr', 'SPHS1Ptr', '3MOPt2im', '6THFtm', 'EBASTINEtr', 'ARTCOAL1', 'EX_thf_e', 'MCD', 'ACTNMO', 'GND', 'MI134P4P', 'NMNS', 'SARDHm', 'EX_his__L_e', 'DHEASULT', 'GGLUCT', 'DNDPt42m', 'PGPP_hs', 'DM_datp_m', 'DM_dgtp_n', 'PIK3n', 'GLUt6', 'ARTPLM1m', 'ENGASE2ly', 'CYSTSERex', 'GLRASE', 'UDPG1P', 'HGNTOR', 'FORtr', 'PI4PLCn', 'THFtl', 'CLFORtex', '6DHFtl', 'DNDPt5m', 'HSD3B3r', 'NADtru', 'PI45P4P', 'DCTPtn', 'ATPasel', '10FTHF7GLUtl', 'THMDt4', 'EX_4nphsf_e', '5THFtl', 'ARTFR212', 'PE_HSter', 'EX_pe_hs_e', '3SALAOX', 'ACALDtx', 'O2ter', 'DURAD', 'HIStiDF', 'EX_etoh_e', 'EX_retinol_9_cis_e', '5DHFtl', 'DRBK', 'EX_cysi__L_e', 'NICRNS', 'FBP', 'CLFORtex2', 'PAFS', 'URATEt', 'PPAtm', 'SPHK21c', '4PYRDX', 'DOLGPP_Ler', 'ARTFR203', 'DOLGLCP_Lter', 'NACASPAH', 'GLACter', 'ESTRONESt2', 'EX_mepi_e', 'RNMK', 'EX_ocdca_e', 'URIt5', 'DNDPt18m', 'PI4PP', 'PIK5n', 'RTOT_2', 'MCLACCYSR', 'CSNATr', 'CYSTGL', 'PA_HStn', 'EX_tcynt_e', 'PGL', 'EX_orn_e', 'PROSTGE1t', 'DOLGLCP_Uter', 'RTOT2', 'SLCBK1', 'DOLP_Uter', 'THFtm', 'EX_ile__L_e', 'MI1PS', 'EX_urea_e', 'DCSPTN1COAtx', 'ADRNCOAtx', 'GLUVESSEC', 'EX_tettet6_e', 'ARTFR45', 'ARTFR44', 'DKMPPD', 'BTNDe', '24_25DHVITD2tm', 'DSAT', 'GLYATm', 'LRAT1', '2MCITt', 'ILETA', 'GCHOLAt2', 'C3STKR2r', '6DHFtm', 'NORANMT', 'DHFtl', 'PDE4', 'DUMPtn', 'CH25H', 'PItx', 'TDP', '3AIBt', 'EX_ocdcea_e', 'ARTFR204', 'DHORD9', 'EX_10fthf_e', 'UDPGNP', 'PNTOt5', 'MI1P_Dtn', '7THFtm', 'DNDPt51m', 'MMTSADm', 'PPPG9tm', 'DHORTS', 'MEPIVESSte', 'EX_ebastine_e', 'AGDC', 'NADPtxu', 'BHBtm', 'GACMTRc', '6THFtl', 'AACTOOR', 'MI13PP', 'EX_lnlnca_e', 'EX_leu__L_e', 'DUDPtn', 'GLYtm', 'PPBNGS', 'RETH2', 'EX_ptdca_e', 'EX_btn_e', '24_25DHVITD2t', 'ARTFR32', 'CRMPte', 'SPH1Pter', 'NCKt', 'EX_4nph_e', 'ARTFR53', 'ARTFR33', 'EX_2425dhvitd2_e', 'H2CO3D2', 'SPMDOX', '3HBCOAHLm', 'DATPtn', 'PHYCBOXL', 'XOLTRI25te', 'ASNtm', 'ARTFR54', 'P4507B11r', 'PPAn', 'BDHm', 'FUMSO4tm', 'KDNH', 'UREAtm', 'EBASTINEOHte', '10FTHF6GLUtm', 'NADtn', 'PI45P5Pn', '7THFtl', 'EX_thm_e', 'BTNt3i', 'EX_ala_B_e', 'EX_4pyrdx_e', 'CHOLATEt2', 'GTMLTe', 'HISTAtu', 'FDH', 'CO2ter', 'BCDO', 'PROD2', '10FTHF5GLUtl', 'ACOAD8m', 'CEPTC', 'HXANtx', 'O2tn', '3AIBTm', 'GPDDA1', 'DNDPt4m', 'EX_thmtp_e', 'GLYK', 'EX_bilirub_e', 'DNDPt31m', 'VALt5m', 'HAS1', 'ARTPLM3m', 'EX_met__L_e', 'PTDCAt', 'DOLGPP_Uer', 'TETPENT6t', 'NADPHtru', 'EX_dopasf_e', 'EX_oxa_e', 'GUAD', 'ARTFR202', 'OPAH', 'HAtly', 'DNDPt3m', 'PItn', 'PRDXl', 'PI5P4Kn', 'RETH1', 'DOLICHOL_Lter', 'O2Stn', 'DGTPtn', 'CBPS', 'PI4P3Kn', 'UROLACer', 'TCHOLAt2', 'ARTFR13', 'TRDR', 'EX_2425dhvitd3_e', 'ARTFR42', 'DGSNtm', 'LNLNCAt', 'XANtx', 'GLUCYS', 'EX_co_e', 'EX_4abut_e', 'RTOT3', 'MERCPLACCYSt', 'EX_cmp_e', 'GABAVESSEC', 'EX_arg__L_e', 'NDP6', 'COAtp', 'TMDPPK', 'H2O2tly', 'DINt', 'ADNK1m', 'EX_crmp_hs_e', 'NDP7er', 'NMNtn', 'CSNATm', 'ETOHtx', 'DHFtm', 'EX_cyan_e', 'SPHINGStr', 'PACCOAL', 'EX_trp__L_e', 'DGULND', 'DNDPt2m', 'XYLTD_D', 'FCLTm', '4MOPt2im', 'ASPNATm', 'UDPG4E', 'EX_7dhf_e', '4NPHte', 'RETHe', 'TETPENT3t', 'ACNML', 'DPCOAPP', 'PIPLCn', 'NRPPHRSFt', 'FATP9t', 'ETOHt', 'GUAPRT', '10FTHF7GLUtm', 'EX_creat_e', 'ARTFR205', 'PI34P4Pn', 'SERHL', 'RTOT5', 'RAI2', '3SPYRSP', 'ARTFR57', 'CITRtm', 'HEXCt', 'ARTFR34', 'MGSA2', 'DNDPt6m', 'FRDPtr', 'ARTFR211', 'EX_bhb_e', 'PI3P4Kn', 'AOBUTDsm', 'ACSm', 'HKt', 'MTRI', 'TCYNTt', 'XOLTRI25tc', 'SARCStm', '13DAMPPOX', 'ARTFR210', 'ARTFR209', 'EX_sl__L_e', 'MCITS', 'PI4P4Pn', 'HESTRATRIOLtr', 'PHEACGLNt', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'MDRPD', 'PI45P3Kn', 'NADPHtxu', '4NPHSFte', 'EX_biocyt_e', 'DOLP_Lter', 'ADPtx', 'LRAT2', 'PROD2m', 'EX_ebastineoh_e', 'PI34P5Kn', 'GLNtm', 'CLOHtex2', 'VBOF', '10FTHF5GLUtm', 'ARGtm', 'EX_vitd3_e', '34HPPOR', 'DNDPt19m', 'biomass_mac', 'ADCim', 'EBASTINEte', 'GSNt4', 'DNDPt54m', 'KHK2', '2AMACHYD', 'EX_sarcs_e', 'DNDPt32m', 'DNDPt1m', 'ETFQO', 'FE2tm', 'MMSAD1m', 'DOLPH_Ler', 'CEPTE', 'GLNLASEer', 'DM_dctp_n', 'EBASTINEOHtr', 'RETH2e', 'DESAT22_1p', 'AHCYStr', 'FUMSO3tm', 'NACASPtm', '5AOPtm', 'AMETr', 'DOPASFt', 'GLCMter', 'PIt2m', 'EX_7thf_e', 'N2M2NMASNtly', '3AIBtm', 'EX_5mthf_e', 'EX_retinol_cis_11_e', 'CYTDt4', 'LEUt5m', 'GLYAMDTRc', 'CHSTEROLt2', 'GULLACter', '2AMACSULT', 'EX_urate_e', 'ATPtn', 'EX_tymsf_e', 'RETI1', 'CYOOm3', 'ARTFR43', 'DM_Asn_X_Ser_Thr_l', 'INOSTO', 'THMTPt']\n", + "Reaction EX_bhb_e is not in Z\n", + "1537\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1537\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 889 (119 core, 770 non-core); Num. remaining: 592\n", + "Reaction no. 407\n", + "Attempting to remove reaction: EX_bvite_e ...\n", + "Initial PM reactions: 1537\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5263500000000931\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['PUNP1'], inactive_NC:['DM_bvite_c', 'BVITEt', 'EX_bvite_e']\n", + "Reaction EX_bvite_e is not in Z\n", + "1537\n", + "1537\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 889 (119 core, 770 non-core); Num. remaining: 591\n", + "Reaction no. 408\n", + "Attempting to remove reaction: EX_ebastine_e ...\n", + "Initial PM reactions: 1537\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2046999999997752\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: [], inactive_NC:['EX_pi_e', 'EBASTINEte', 'EX_ebastineoh_e', 'P4504F123r', 'EBASTINEtr', 'EBASTINEOHtr', 'EBASTINEOHte', 'EX_ebastine_e']\n", + "Reaction EX_ebastine_e is not in Z\n", + "1537\n", + "1537\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 889 (119 core, 770 non-core); Num. remaining: 590\n", + "Reaction no. 409\n", + "Attempting to remove reaction: EX_ebastineoh_e ...\n", + "Initial PM reactions: 1537\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2052409999996598\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: [], inactive_NC:['EBASTINEtr', 'EBASTINEOHtr', 'EBASTINEte', 'EBASTINEOHte', 'EX_ebastineoh_e', 'P4504F123r', 'EX_ebastine_e']\n", + "Reaction EX_ebastineoh_e is not in Z\n", + "1537\n", + "1537\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1530\n", + "Num. removed: 896 (119 core, 777 non-core); Num. remaining: 587\n", + "Reaction no. 410\n", + "Attempting to remove reaction: EX_mthgxl_e ...\n", + "Initial PM reactions: 1530\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2050229999999829\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GLCt1', 'GLUt2m', 'SERtN1'], inactive_NC:['MTHGXLt', 'EX_mthgxl_e']\n", + "Reaction EX_mthgxl_e is not in Z\n", + "1530\n", + "1530\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 896 (119 core, 777 non-core); Num. remaining: 586\n", + "Reaction no. 411\n", + "Attempting to remove reaction: EX_n2m2nmasn_e ...\n", + "Initial PM reactions: 1530\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5208900000002359\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['AHEXASE2ly', 'GASNASE2ly', 'NDPK5m'], inactive_NC:['EX_n2m2nmasn_e', 'N2M2NMASNtly', 'ENGASE2ly']\n", + "Reaction EX_n2m2nmasn_e is not in Z\n", + "1530\n", + "1530\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 896 (119 core, 777 non-core); Num. remaining: 585\n", + "Reaction no. 412\n", + "Attempting to remove reaction: EX_hcoumarin_e ...\n", + "Initial PM reactions: 1530\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.480637999999999\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['P4502A6', 'GDHm'], inactive_NC:['EX_hcoumarin_e', 'EX_coumarin_e', 'COUMARINte', 'HCOUMARINte']\n", + "Reaction EX_hcoumarin_e is not in Z\n", + "1530\n", + "1530\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 896 (119 core, 777 non-core); Num. remaining: 584\n", + "Reaction no. 413\n", + "Attempting to remove reaction: EX_nrpphrsf_e ...\n", + "Initial PM reactions: 1530\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1367919999997866\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: [], inactive_NC:['NRPPHRSFt', '3HCO3_NAt', 'NRPPHRSULT', 'EX_nrpphrsf_e']\n", + "Reaction EX_nrpphrsf_e is not in Z\n", + "1530\n", + "1530\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1526\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 580\n", + "Reaction no. 414\n", + "Attempting to remove reaction: EX_hestratriol_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1882839999998396\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['HSD17B7r', 'SERtN1', 'HSD17B8r'], inactive_NC:['P4501B1r', 'HESTRATRIOLtr', 'EX_hestratriol_e', 'ESTRONESt2', 'ESTRONEtr', 'HESTRATRIOLte', 'EX_estrones_e']\n", + "Reaction EX_hestratriol_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 579\n", + "Reaction no. 415\n", + "Attempting to remove reaction: EX_hexc_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5090299999997114\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['FACOAL260'], inactive_NC:['HEXCt', 'ARTFR52', 'EX_hexc_e']\n", + "Reaction EX_hexc_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 578\n", + "Reaction no. 416\n", + "Attempting to remove reaction: EX_hpdca_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4701939999999922\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['HPDCACRNCPT1', 'FACOAL170', 'FAOXC170m', 'HPDCACRNt', 'HPDCACRNCPT2'], inactive_NC:['EX_hpdca_e', 'HPDCAt']\n", + "Reaction EX_hpdca_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 577\n", + "Reaction no. 417\n", + "Attempting to remove reaction: EX_htaxol_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1784059999999954\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['PUNP1'], inactive_NC:['TAXOLte', 'HTAXOLte', 'P4502C8', 'EX_taxol_e', 'EX_htaxol_e']\n", + "Reaction EX_htaxol_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 576\n", + "Reaction no. 418\n", + "Attempting to remove reaction: EX_octa_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3413609999997789\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['FACOAL80'], inactive_NC:['EX_octa_e', 'OCTAt']\n", + "Reaction EX_octa_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 575\n", + "Reaction no. 419\n", + "Attempting to remove reaction: EX_pheacgln_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4675449999999728\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['PEAMNO', 'PUNP5', 'ALDD19x_P', 'ALDD19xr'], inactive_NC:['PACCOAL', 'EX_pheacgln_e', 'PHEACGLNt', 'PHACCOAGLNAC', 'PHYCBOXL']\n", + "Reaction EX_pheacgln_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 574\n", + "Reaction no. 420\n", + "Attempting to remove reaction: EX_ppa_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4380510000000868\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['ACS2', 'ACCOAL'], inactive_NC:['PPAtr', 'PPAtm', 'EX_ppa_e', 'ACCOALm']\n", + "Reaction EX_ppa_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 573\n", + "Reaction no. 421\n", + "Attempting to remove reaction: EX_lnlc_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 19 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2270630000002711\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 20 , inactive_C: ['LNLCCPT2', 'DLNLCGCPT1', 'DESAT20_1', 'DESAT18_9', 'DLNLCGCRNt', 'FAOXC2031836m', 'LNLCCRNt', 'DLNLCGCPT2', 'LNLNCGCRNt', 'LNLNCGCPT1', 'LNLNCGCPT2', 'LNLCCPT1', 'FAEL183', 'FACOAL1821', 'FAOXC182806m'], inactive_NC:['ARTFR205', 'ARTFR210', 'EX_lnlc_e', 'LNLCt', 'ARTFR203']\n", + "Reaction EX_lnlc_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 572\n", + "Reaction no. 422\n", + "Attempting to remove reaction: EX_lnlnca_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 33 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2676289999999426\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 34 , inactive_C: ['STRDNCCPT1', 'NKCC2t', 'FACOAL1832', '2HBO', 'LNLNCACPT2', 'FAEL205', 'FAEL184', '2HBt2', 'EICOSTETCPT2', 'STRDNCCPT2', 'TMNDNCCRNt', 'LNLNCACRNt', 'EICOSTETCRNt', 'SERtN1', 'EICOSTETCPT1', 'NDPK5m', 'FAOXC204184m', 'STRDNCCRNt', 'DESAT20_2', 'FAOXC183803m', 'LNLNCACPT1', 'TMNDNCCPT1', 'TMNDNCCPT2', 'DESAT18_10'], inactive_NC:['EX_pi_e', 'ARTFR211', 'EX_lnlnca_e', 'ARTFR208', '2HCO3_NAt', 'EX_2hb_e', 'ARTFR53', 'LNLNCAt', 'ARTFR202', 'ARTFR204']\n", + "Reaction EX_lnlnca_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 571\n", + "Reaction no. 423\n", + "Attempting to remove reaction: EX_ptdca_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.478733999999804\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['PTDCACRNCPT1', 'PTDCACRNt', 'FACOAL150', 'PTDCACRNCPT2', 'FAOXC150m'], inactive_NC:['EX_ptdca_e', 'PTDCAt', 'GHMT2r']\n", + "Reaction EX_ptdca_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 570\n", + "Reaction no. 424\n", + "Attempting to remove reaction: EX_pydx_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4688530000003084\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['PYDXDH', 'SERtN1'], inactive_NC:['EX_pi_e', 'EX_4pyrdx_e', 'EX_pydx_e', 'NH4t3r', 'GLYtm', '4PYRDX', 'NAHCO3_HCLt', 'PYDXtr']\n", + "Reaction EX_pydx_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 569\n", + "Reaction no. 425\n", + "Attempting to remove reaction: EX_mepi_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4144000000001142\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['SALMCOM2'], inactive_NC:['EX_mepi_e', 'MEPIVESSte', 'HCO3_NAt']\n", + "Reaction EX_mepi_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 568\n", + "Reaction no. 426\n", + "Attempting to remove reaction: EX_mercplaccys_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2074549999997544\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['MCLORi'], inactive_NC:['MERCPLACCYSt', 'MCLACCYSR', '2HCO3_NAt', 'EX_mercplaccys_e']\n", + "Reaction EX_mercplaccys_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 567\n", + "Reaction no. 427\n", + "Attempting to remove reaction: EX_retinol_9_cis_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.294926999999916\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['RDH2a', 'CREATt4_2_r'], inactive_NC:['RETFAt1', 'EX_creat_e', 'EX_retinol_9_cis_e', 'GLYAMDTRc', 'RETH1e', 'GACMTRc', 'RAI2']\n", + "Reaction EX_retinol_9_cis_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 566\n", + "Reaction no. 428\n", + "Attempting to remove reaction: EX_retinol_cis_11_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5085770000000593\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['RDH1a'], inactive_NC:['EX_pi_e', 'RETI1', 'RETH2e', 'EX_retinol_cis_11_e', 'RETFAt2']\n", + "Reaction EX_retinol_cis_11_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 900 (119 core, 781 non-core); Num. remaining: 565\n", + "Reaction no. 429\n", + "Attempting to remove reaction: EX_taxol_e ...\n", + "Initial PM reactions: 1526\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4276669999999285\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['TAXOLte', 'P4502C8', 'HTAXOLte', 'EX_taxol_e', 'EX_htaxol_e']\n", + "Reaction EX_taxol_e is not in Z\n", + "1526\n", + "1526\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1521\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 564\n", + "Reaction no. 430\n", + "Attempting to remove reaction: EX_retn_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3508230000002186\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['NDPK5m', 'RAI3'], inactive_NC:['DM_13_cis_retn_n', 'ORETNtn2', 'RAtn3', 'RAHY', 'ORETNF2', 'RETNt', 'DM_hretn_n', 'DM_13_cis_oretn_n', 'EX_retn_e', 'HRETNtn']\n", + "Reaction EX_retn_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 563\n", + "Reaction no. 431\n", + "Attempting to remove reaction: EX_tcynt_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.178429000000051\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['MCPST'], inactive_NC:['TCYNTt', 'EX_tcynt_e', 'EX_cyan_e', 'CYANt']\n", + "Reaction EX_tcynt_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 562\n", + "Reaction no. 432\n", + "Attempting to remove reaction: EX_tetpent3_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4973469999999907\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['FACOAL245_2', 'DESAT24_1'], inactive_NC:['EX_tetpent3_e', 'ARTFR57', 'ARTFR55', 'TETPENT3t']\n", + "Reaction EX_tetpent3_e is not in Z\n", + "1521\n", + "1521\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 561\n", + "Reaction no. 433\n", + "Attempting to remove reaction: EX_tetpent6_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.478686999999809\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['FACOAL245_1', 'CREATt4_2_r', 'NKCC2t', 'PUNP1'], inactive_NC:['EX_creat_e', 'ARTFR54', 'GLYAMDTRc', 'EX_tetpent6_e', 'TETPENT6t', 'GACMTRc']\n", + "Reaction EX_tetpent6_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 560\n", + "Reaction no. 434\n", + "Attempting to remove reaction: EX_tettet6_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.443127000000004\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['FACOAL244_1', 'NDPK5m'], inactive_NC:['ARTFR56', 'TETTET6t', 'EX_tettet6_e']\n", + "Reaction EX_tettet6_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 559\n", + "Reaction no. 435\n", + "Attempting to remove reaction: EX_sarcs_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2185410000001866\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['FPGS8m', 'CREATt4_2_r', 'FPGS7m', 'MTHFCm', 'FPGS9m'], inactive_NC:['EX_creat_e', 'SARCStm', 'GLYAMDTRc', 'SARCStex', 'SARDHm', '10FTHF5GLUtm', 'EX_sarcs_e', '10FTHF7GLUtm', 'GACMTRc', '10FTHF6GLUtm']\n", + "Reaction EX_sarcs_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 558\n", + "Reaction no. 436\n", + "Attempting to remove reaction: EX_sl__L_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5835189999997965\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['LCYSTAT', 'SLDx'], inactive_NC:['3SALAOX', '2AMACSULT', 'SLDt', 'EX_sl__L_e']\n", + "Reaction EX_sl__L_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 557\n", + "Reaction no. 437\n", + "Attempting to remove reaction: EX_ttdca_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 35 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7253609999997934\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 36 , inactive_C: ['THYMDt1', 'FACOAL140', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'SERtN1', 'PUNP1', 'DGAT', 'DCYTD', 'RNDR4'], inactive_NC:['EX_ttdca_e', 'CEPTE', 'PA_HSter', 'TTDCAtr', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'PCHOLPr_hs', 'PGPP_hs', 'DUMPtn', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', '2HCO3_NAt', 'NDP6']\n", + "Reaction EX_ttdca_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 556\n", + "Reaction no. 438\n", + "Attempting to remove reaction: EX_tymsf_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1743200000000797\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TYMSULT'], inactive_NC:['EX_tymsf_e', 'TYMSFt']\n", + "Reaction EX_tymsf_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 555\n", + "Reaction no. 439\n", + "Attempting to remove reaction: EX_urate_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 19 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1668949999998404\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 20 , inactive_C: ['PUNP7', 'NTD10', 'DCSPTN1CPT1', 'FAOXC2251836m', 'DCSPTN1CPT2', 'XAO2x', 'XANDp', 'XAOx', 'DCSPTN1CRNt', 'FAOXC2252053m'], inactive_NC:['URATEtx', 'ADRNCOAtx', 'ARTFR212', 'EX_urate_e', 'HXANtx', 'GUAD', 'DESAT22_1p', 'DCSPTN1COAtx', 'XANtx', 'URATEt']\n", + "Reaction EX_urate_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 554\n", + "Reaction no. 440\n", + "Attempting to remove reaction: EX_vitd3_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2526429999998072\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['24_25VITD3Hm', 'SERtN1'], inactive_NC:['24_25DHVITD3tm', 'EX_2425dhvitd3_e', '24_25DHVITD3t', 'EX_vitd3_e', 'VITD3Hm']\n", + "Reaction EX_vitd3_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 553\n", + "Reaction no. 441\n", + "Attempting to remove reaction: EX_xolest_hs_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4839779999997518\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['SOAT12', 'SOAT11'], inactive_NC:['EX_xolest_hs_e', 'XOLESTte']\n", + "Reaction EX_xolest_hs_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 552\n", + "Reaction no. 442\n", + "Attempting to remove reaction: EX_xoltri25_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5144089999998869\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['NKCC2t', 'GDHm'], inactive_NC:['P4507B11r', 'EX_xoltri25_e', 'EX_h_e', 'CH25H', 'XOLTRI25tc', 'XOLTRI25te']\n", + "Reaction EX_xoltri25_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 905 (119 core, 786 non-core); Num. remaining: 551\n", + "Reaction no. 443\n", + "Attempting to remove reaction: EX_yvite_e ...\n", + "Initial PM reactions: 1521\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.247262000000319\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['DM_yvite_c', 'EX_yvite_e', 'YVITEt']\n", + "Reaction EX_yvite_e is not in Z\n", + "1521\n", + "1521\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1518\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 549\n", + "Reaction no. 444\n", + "Attempting to remove reaction: PHEACGLNt ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1820689999999558\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['NKCC2t', 'GDHm', 'PEAMNO', 'ALDD19xr', 'ALDD19x_P'], inactive_NC:['PACCOAL', 'EX_pheacgln_e', 'PHEACGLNt', '2HCO3_NAt', 'PHACCOAGLNAC', 'PHYCBOXL']\n", + "Reaction PHEACGLNt is not in Z\n", + "1518\n", + "1518\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 548\n", + "Reaction no. 445\n", + "Attempting to remove reaction: 3AIBt ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5045159999999669\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['HCO3_CLt'], inactive_NC:['3AIBTm', 'EX_3aib_e', '3AIBt', '3AIBtm']\n", + "Reaction 3AIBt is not in Z\n", + "1518\n", + "1518\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 547\n", + "Reaction no. 446\n", + "Attempting to remove reaction: EX_arab__L_e ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4608829999997397\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['ARABR'], inactive_NC:['ARAB_Lt', 'ABTt', 'EX_arab__L_e', 'EX_abt_e']\n", + "Reaction EX_arab__L_e is not in Z\n", + "1518\n", + "1518\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 546\n", + "Reaction no. 447\n", + "Attempting to remove reaction: EX_co2_e ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 545\n", + "Reaction no. 448\n", + "Attempting to remove reaction: EX_co_e ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 544\n", + "Reaction no. 449\n", + "Attempting to remove reaction: EX_etoh_e ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2766190000002098\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['ALCD2x', 'PUNP5', 'ALCD2y', 'SERtN1', 'CAT2p'], inactive_NC:['EX_etoh_e', 'ETOHMO', 'ETOHt', 'ACALDtx', 'ETOHtx']\n", + "Reaction EX_etoh_e is not in Z\n", + "1518\n", + "1518\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 543\n", + "Reaction no. 450\n", + "Attempting to remove reaction: GLACter ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 542\n", + "Reaction no. 451\n", + "Attempting to remove reaction: GULLACter ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 541\n", + "Reaction no. 452\n", + "Attempting to remove reaction: GULNter ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 540\n", + "Reaction no. 453\n", + "Attempting to remove reaction: HESTRATRIOLte ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2282270000000608\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['HSD17B7r', 'HSD17B8r'], inactive_NC:['P4501B1r', 'HESTRATRIOLtr', 'EX_hestratriol_e', 'ESTRONESt2', 'ESTRONEtr', 'HESTRATRIOLte', 'EX_estrones_e']\n", + "Reaction HESTRATRIOLte is not in Z\n", + "1518\n", + "1518\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 539\n", + "Reaction no. 454\n", + "Attempting to remove reaction: XOLTRI25te ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4582919999998012\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['SERtN1', 'NKCC2t'], inactive_NC:['P4507B11r', 'EX_xoltri25_e', 'CH25H', 'XOLTRI25tc', 'XOLTRI25te']\n", + "Reaction XOLTRI25te is not in Z\n", + "1518\n", + "1518\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 908 (119 core, 789 non-core); Num. remaining: 538\n", + "Reaction no. 455\n", + "Attempting to remove reaction: 25HVITD2t ...\n", + "Initial PM reactions: 1518\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3575689999997849\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['25HVITD2t']\n", + "Reaction 25HVITD2t is not in Z\n", + "1518\n", + "1518\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1517\n", + "Num. removed: 909 (119 core, 790 non-core); Num. remaining: 537\n", + "Reaction no. 456\n", + "Attempting to remove reaction: 25HVITD2tin ...\n", + "Initial PM reactions: 1517\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2559270000001561\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['24_25VITD2Hm', 'NDPK5m'], inactive_NC:['25HVITD2tin', 'EX_25hvitd2_e', '24_25DHVITD2tm', '24_25DHVITD2t', 'EX_2425dhvitd2_e']\n", + "Reaction 25HVITD2tin is not in Z\n", + "1517\n", + "1517\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 909 (119 core, 790 non-core); Num. remaining: 536\n", + "Reaction no. 457\n", + "Attempting to remove reaction: 25HVITD3t ...\n", + "Initial PM reactions: 1517\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1822659999997995\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['PUNP1', 'GDHm'], inactive_NC:['25HVITD3tin', '25HVITD3t']\n", + "Reaction 25HVITD3t is not in Z\n", + "1517\n", + "1517\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 909 (119 core, 790 non-core); Num. remaining: 535\n", + "Reaction no. 458\n", + "Attempting to remove reaction: 25HVITD3tin ...\n", + "Initial PM reactions: 1517\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1876240000001417\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['PUNP1', 'GDHm'], inactive_NC:['25HVITD3tin', '25HVITD3t']\n", + "Reaction 25HVITD3tin is not in Z\n", + "1517\n", + "1517\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 909 (119 core, 790 non-core); Num. remaining: 534\n", + "Reaction no. 459\n", + "Attempting to remove reaction: 2MCITt ...\n", + "Initial PM reactions: 1517\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 13 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.47057199999972\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 14 , inactive_C: ['ACS2', 'ACITL', 'CREATt4_2_r', 'SERtN1', 'ACCOAL'], inactive_NC:['2MCITt', 'EX_creat_e', 'GLYAMDTRc', 'NH4t3r', 'OBDHc', '2HCO3_NAt', 'GACMTRc', 'EX_2mcit_e', 'MCITS']\n", + "Reaction 2MCITt is not in Z\n", + "1517\n", + "1517\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 909 (119 core, 790 non-core); Num. remaining: 533\n", + "Reaction no. 460\n", + "Attempting to remove reaction: 24_25DHVITD2t ...\n", + "Initial PM reactions: 1517\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.511634999999842\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['24_25VITD2Hm'], inactive_NC:['25HVITD2tin', 'EX_25hvitd2_e', '2HCO3_NAt', '24_25DHVITD2tm', '24_25DHVITD2t', 'EX_2425dhvitd2_e']\n", + "Reaction 24_25DHVITD2t is not in Z\n", + "1517\n", + "1517\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 909 (119 core, 790 non-core); Num. remaining: 532\n", + "Reaction no. 461\n", + "Attempting to remove reaction: 24_25DHVITD3t ...\n", + "Initial PM reactions: 1517\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1448749999999563\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['24_25VITD3Hm'], inactive_NC:['24_25DHVITD3tm', 'EX_2425dhvitd3_e', '24_25DHVITD3t', 'EX_vitd3_e', 'VITD3Hm']\n", + "Reaction 24_25DHVITD3t is not in Z\n", + "1517\n", + "1517\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 909 (119 core, 790 non-core); Num. remaining: 531\n", + "Reaction no. 462\n", + "Attempting to remove reaction: BVITEt ...\n", + "Initial PM reactions: 1517\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2419509999999718\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['GLUt2m'], inactive_NC:['DM_bvite_c', 'BVITEt', 'EX_bvite_e']\n", + "Reaction BVITEt is not in Z\n", + "1517\n", + "1517\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 909 (119 core, 790 non-core); Num. remaining: 530\n", + "Reaction no. 463\n", + "Attempting to remove reaction: HRETNtn ...\n", + "Initial PM reactions: 1517\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2539119999996728\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['RAHY', 'HRETNtn', 'DM_hretn_n']\n", + "Reaction HRETNtn is not in Z\n", + "1517\n", + "1517\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1514\n", + "Num. removed: 912 (119 core, 793 non-core); Num. remaining: 528\n", + "Reaction no. 464\n", + "Attempting to remove reaction: MERCPLACCYSt ...\n", + "Initial PM reactions: 1514\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4587929999997868\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['MCLORi'], inactive_NC:['MERCPLACCYSt', 'EX_mercplaccys_e', 'MCLACCYSR']\n", + "Reaction MERCPLACCYSt is not in Z\n", + "1514\n", + "1514\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 912 (119 core, 793 non-core); Num. remaining: 527\n", + "Reaction no. 465\n", + "Attempting to remove reaction: ORETNtn2 ...\n", + "Initial PM reactions: 1514\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4798209999999017\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['DM_13_cis_oretn_n', 'ORETNtn2', 'ORETNF2']\n", + "Reaction ORETNtn2 is not in Z\n", + "1514\n", + "1514\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1511\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 525\n", + "Reaction no. 466\n", + "Attempting to remove reaction: RETFAt1 ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1645400000002155\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['RDH2a', 'NKCC2t'], inactive_NC:['RETFAt1', 'RAI2', 'RETH1e', 'EX_retinol_9_cis_e']\n", + "Reaction RETFAt1 is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 524\n", + "Reaction no. 467\n", + "Attempting to remove reaction: RETFAt2 ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1191430000003493\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['RDH1a', 'NKCC2t'], inactive_NC:['RETI1', 'RETH2e', 'EX_retinol_cis_11_e', 'RETFAt2']\n", + "Reaction RETFAt2 is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 523\n", + "Reaction no. 468\n", + "Attempting to remove reaction: URATEt ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 25 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4645409999998265\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 26 , inactive_C: ['PUNP7', 'NTD10', 'DCSPTN1CPT1', 'FAOXC2251836m', 'DCSPTN1CPT2', 'XAO2x', 'CREATt4_2_r', 'XANDp', 'XAOx', 'GLUt2m', 'MTHFD2m', 'DCSPTN1CRNt', 'FAOXC2252053m'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'URATEtx', 'ADRNCOAtx', 'ARTFR212', 'EX_urate_e', 'HXANtx', 'GUAD', 'DESAT22_1p', 'GACMTRc', 'DCSPTN1COAtx', 'XANtx', 'URATEt']\n", + "Reaction URATEt is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 522\n", + "Reaction no. 469\n", + "Attempting to remove reaction: VITD3t ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4464960000000247\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['NDPK5m'], inactive_NC:['2HCO3_NAt', 'VITD3t']\n", + "Reaction VITD3t is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 521\n", + "Reaction no. 470\n", + "Attempting to remove reaction: VITD3t2 ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 13 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1950379999998404\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 14 , inactive_C: ['24_25VITD3Hm', 'CREATt4_2_r', 'PUNP1'], inactive_NC:['24_25DHVITD3tm', 'EX_creat_e', 'GLYAMDTRc', 'EX_2425dhvitd3_e', 'VITD3t', '24_25DHVITD3t', 'VITD3t2', '2HCO3_NAt', 'EX_vitd3_e', 'GACMTRc', 'VITD3Hm']\n", + "Reaction VITD3t2 is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 520\n", + "Reaction no. 471\n", + "Attempting to remove reaction: EX_35cgmp_e ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2223449999996774\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CGMPt', 'CREATt4_2_r'], inactive_NC:['GACMTRc', 'EX_creat_e', 'EX_35cgmp_e', 'GLYAMDTRc']\n", + "Reaction EX_35cgmp_e is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 519\n", + "Reaction no. 472\n", + "Attempting to remove reaction: EX_camp_e ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2002410000000054\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['CAMPt'], inactive_NC:['EX_camp_e']\n", + "Reaction EX_camp_e is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 518\n", + "Reaction no. 473\n", + "Attempting to remove reaction: COUMARINte ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4446939999997994\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['P4502A6'], inactive_NC:['EX_hcoumarin_e', 'EX_coumarin_e', 'COUMARINte', 'HCOUMARINte']\n", + "Reaction COUMARINte is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 517\n", + "Reaction no. 474\n", + "Attempting to remove reaction: COt ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 516\n", + "Reaction no. 475\n", + "Attempting to remove reaction: HCOUMARINte ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4267449999997552\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['NDPK5m', 'PUNP1', 'P4502A6'], inactive_NC:['EX_pi_e', 'EX_coumarin_e', 'COUMARINte', 'HCOUMARINte', 'EX_hcoumarin_e']\n", + "Reaction HCOUMARINte is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 515\n", + "Reaction no. 476\n", + "Attempting to remove reaction: HPACtr ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2623950000001969\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['TYROXDAc', '4HOXPACDOX_NADP'], inactive_NC:['EX_4hphac_e', 'HPACtr']\n", + "Reaction HPACtr is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 514\n", + "Reaction no. 477\n", + "Attempting to remove reaction: CRMPte ...\n", + "Initial PM reactions: 1511\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.183622000000014\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['CERK'], inactive_NC:['EX_crmp_hs_e', 'CRMPte']\n", + "Reaction CRMPte is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 513\n", + "Reaction no. 478\n", + "Attempting to remove reaction: EX_4abut_e ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4173469999996087\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['ABUTD', 'BAMPPALDOX', 'NDPK5m'], inactive_NC:['13DAMPPOX', 'EX_4abut_e', 'SPMDOX', 'PTRCOX1', 'GABAVESSEC']\n", + "Reaction EX_4abut_e is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 512\n", + "Reaction no. 479\n", + "Attempting to remove reaction: O2St ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 86 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6104960000002393\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 87 , inactive_C: ['GCALDD', 'CATp', 'SPODM', 'FAOXC161802m', 'DUTPDPn', 'C161CPT22', 'FBA4', 'XAOx', 'ALAR', 'RNDR4', 'GLYCLTDy', 'DCSPTN1CPT1', 'GDHm', 'PI345P3Pn', 'CAT2p', 'PYRt2p', 'PUNP7', 'DCSPTN1CPT2', 'C161CRN2t', 'C161CPT12', 'FAOXC2252053m', 'GLXO1', 'NTD10', 'FAOXC2251836m', 'XAO2x', 'SPODMx', 'XANDp', 'NDPK6n', 'SPODMn', 'DCSPTN1CRNt', 'DAGKn_hs'], inactive_NC:['PA_HStn', 'H2Otp', 'GLYCTO1p', 'ASCBOX', 'PMTCOAtx', 'GLXtp', 'ETOHtx', 'DESAT22_1p', 'EX_oxa_e', 'GUAD', 'DCSPTN1COAtx', 'URATEt', 'PI45P5Pn', 'DALAxt', 'ARTFR61', 'O2St', 'PIK4n', 'PI4P4Pn', 'H2O2tn', 'ADRNCOAtx', 'GLYCLTtp', 'DUDPtn', 'RTOT6', 'PI5P4Kn', 'PI34P4Pn', 'PI45P3Kn', 'DALAOXx', 'MI14Ptn', 'PIK3n', 'O2Stn', 'ACOAO7p', 'PI4P3Kn', 'HDD2COAtx', 'URATEtx', 'EX_o2s_e', 'PI4PLCn', 'PI3P3Pn', 'PI34P3Pn', 'DUMPtn', 'PI34P5Kn', 'HXANtx', 'O2tn', 'PAIL_HStn', 'PI345P5Pn', 'NH4tp', 'XANtx', 'O2Stx', 'ARTFR212', 'PI3P4Kn', 'MI1P_Dtn', 'EX_urate_e', 'KHK2', 'PIPLCn', 'ACALDtx', 'PI4P5Kn', 'PIK5n']\n", + "Reaction O2St is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 511\n", + "Reaction no. 480\n", + "Attempting to remove reaction: EX_pyr_e ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.278874999999971\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['PYRt2'], inactive_NC:['EX_pyr_e']\n", + "Reaction EX_pyr_e is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 510\n", + "Reaction no. 481\n", + "Attempting to remove reaction: EX_lac__L_e ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2740410000005795\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['LDH_L', 'L_LACt2r'], inactive_NC:['EX_lac__L_e']\n", + "Reaction EX_lac__L_e is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 509\n", + "Reaction no. 482\n", + "Attempting to remove reaction: EX_thm_e ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.334023000000343\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['5MTHFt', 'CREATt4_2_r', 'THMt3', 'FOLR2'], inactive_NC:['EX_thm_e', 'FOLt2', 'EX_creat_e', 'GLYAMDTRc', 'EX_thmtp_e', 'CLOHtex2', 'EX_5mthf_e', 'EX_fol_e', '2HCO3_NAt', 'GACMTRc', 'THMTPt']\n", + "Reaction EX_thm_e is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 508\n", + "Reaction no. 483\n", + "Attempting to remove reaction: EX_2hb_e ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.493995000000723\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['2HBt2', '2HBO'], inactive_NC:['EX_2hb_e']\n", + "Reaction EX_2hb_e is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 507\n", + "Reaction no. 484\n", + "Attempting to remove reaction: EX_lac__D_e ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4148239999994985\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['D_LACt2', 'LCADi_D', 'LGTHL', 'GLYOX'], inactive_NC:['EX_lac__D_e']\n", + "Reaction EX_lac__D_e is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 506\n", + "Reaction no. 485\n", + "Attempting to remove reaction: EX_but_e ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 12 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2038359999996828\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 13 , inactive_C: ['BUTt2r', 'GDHm', 'CREATt4_2_r', 'HACD1m', 'ACOAD1fm', 'BUTt2m', 'ECOAH1m'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'NH4t3r', 'FACOAL40im', 'GACMTRc', 'EX_but_e']\n", + "Reaction EX_but_e is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 915 (119 core, 796 non-core); Num. remaining: 505\n", + "Reaction no. 486\n", + "Attempting to remove reaction: RETt ...\n", + "Initial PM reactions: 1511\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1505770000003395\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['RETFAt', 'RETt', 'RETHe']\n", + "Reaction RETt is not in Z\n", + "1511\n", + "1511\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1508\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 503\n", + "Reaction no. 487\n", + "Attempting to remove reaction: MEOHtly ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 256 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7788740000005419\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 257 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'FPGS8', 'FPGS7', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'GGH_7THFl', 'CERT1rt', 'GGH_5THFl', 'SQLSr', 'FPGS4', 'C4STMO2r', 'MTHFCm', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'ACNAM9PL2', 'SOAT12', 'GGH_10FTHF6GLUl', 'GALUi', 'NDPK6n', 'FPGS9m', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'FPGS9', 'G6Pter', 'FPGS5m', 'GGH_10FTHF7GLUl', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'GASNASE2ly', 'NDPK5m', 'HMGCOAS', 'UDPGD', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'FPGS6m', 'LSTO1r', 'GGH_7DHFl', 'DUTPDPn', 'FPGSm', 'AHEXASE2ly', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'FPGS3', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'FPGS3m', 'LSTO2r', 'FPGS7m', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'FPGS2m', 'HEX4', 'A_MANASEly', 'MEVK1x', 'SQLEr', 'SBPP1er', 'NTD3', 'FPGS8m', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'GGH_5DHFl', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'FPGS6', 'GLGNS1', 'UGCG', 'FPGS4m', 'GGH_10FTHF5GLUl', 'PSSA2_hs', 'FPGS', 'DMATTx', 'DHCR242r', 'DHCRD2', 'FPGS5', 'FPGS2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'GGH_6DHFl', 'HSD17B9r', 'DHCR243r', 'GGH_6THFl'], inactive_NC:['H2O2tly', 'ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'THFtm', 'NDP7er', '7DHFtm', 'DHFtm', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', '6DHFtm', 'DHFtl', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', '10FTHFtl', '7THFtm', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'MANtly', 'DM_kdn_c', 'NADPtxu', '7DHFtl', '10FTHF7GLUtm', 'DM_dctp_m', 'EX_estrones_e', '6THFtl', 'DUDPtn', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'SARCStex', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'B_MANNASEly', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', '6THFtm', 'XOLTRI25tc', 'XOLTRI25te', 'SARCStm', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'SARDHm', 'KDNH', '10FTHF6GLUtm', '7THFtl', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'ENGASE2ly', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', '10FTHF5GLUtl', 'MEOHtly', 'THFtl', '6DHFtl', 'NADtru', 'HSD3B3r', 'DNDPt52m', '10FTHF5GLUtm', 'DCTPtn', '34HPPOR', 'ATPasel', '10FTHF7GLUtl', 'THMDt4', 'biomass_mac', 'PE_HSter', '5THFtl', 'EX_pe_hs_e', 'DNDPt54m', 'EX_sarcs_e', 'HAS1', 'O2ter', 'DOLPH_Ler', 'EX_n2m2nmasn_e', '5DHFtl', 'NADPtru', 'HAS2', '10FTHF6GLUtl', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'DM_dctp_n', 'AHCYStr', '5THFtm', 'GLUt7l', 'HAtly', 'PRDXl', 'EX_thymd_e', 'SPHK21c', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'N2M2NMASNtly', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'ACGAMtly', 'FALDtly', 'DM_Asn_X_Ser_Thr_l', 'NDP6', 'COAtp']\n", + "Reaction MEOHtly is not in Z\n", + "1508\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 502\n", + "Reaction no. 488\n", + "Attempting to remove reaction: ABTt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.456543000000238\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['PUNP1', 'ARABR'], inactive_NC:['ARAB_Lt', 'ABTt', 'EX_arab__L_e', 'EX_abt_e']\n", + "Reaction ABTt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 501\n", + "Reaction no. 489\n", + "Attempting to remove reaction: ARAB_Lt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.448395999999775\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['ARABR'], inactive_NC:['ARAB_Lt', 'ABTt', 'EX_arab__L_e', 'EX_abt_e']\n", + "Reaction ARAB_Lt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 500\n", + "Reaction no. 490\n", + "Attempting to remove reaction: 34DHOXPEGt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2999760000002425\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['PIt8', '34DHOXPEGOX', '41R1H2MAE12BOOX', 'SFGTHi', '41R2A1H12BOOX', 'FALDH'], inactive_NC:['MAOX', '34DHOXPEGt', 'EX_34dhoxpeg_e']\n", + "Reaction 34DHOXPEGt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 499\n", + "Reaction no. 491\n", + "Attempting to remove reaction: SLDt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.217899999999645\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['LCYSTAT', 'SLDx'], inactive_NC:['3SALAOX', '2AMACSULT', 'SLDt', 'EX_sl__L_e']\n", + "Reaction SLDt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 498\n", + "Reaction no. 492\n", + "Attempting to remove reaction: CYANt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4393309999995836\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['CREATt4_2_r', 'PUNP1', 'MCPST'], inactive_NC:['EX_pi_e', 'EX_tcynt_e', 'EX_creat_e', 'GLYAMDTRc', 'CYANt', 'GACMTRc', 'EX_cyan_e', 'TCYNTt']\n", + "Reaction CYANt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 497\n", + "Reaction no. 493\n", + "Attempting to remove reaction: TCYNTt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3955260000002454\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['MCPST'], inactive_NC:['EX_tcynt_e', 'TCYNTt', 'NAHCO3_HCLt', 'EX_cyan_e', 'CYANt']\n", + "Reaction TCYNTt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 496\n", + "Reaction no. 494\n", + "Attempting to remove reaction: DOPASFt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1839790000003632\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['DOPASULT'], inactive_NC:['DOPASFt', 'EX_dopasf_e']\n", + "Reaction DOPASFt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 495\n", + "Reaction no. 495\n", + "Attempting to remove reaction: GLCURter ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 494\n", + "Reaction no. 496\n", + "Attempting to remove reaction: TYMSFt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.219069999999192\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TYMSULT'], inactive_NC:['EX_tymsf_e', 'TYMSFt']\n", + "Reaction TYMSFt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 493\n", + "Reaction no. 497\n", + "Attempting to remove reaction: 4NPHSFte ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4299760000003516\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['4NPHSULT'], inactive_NC:['EX_4nph_e', '4NPHSFte', '4NPHte', 'EX_4nphsf_e']\n", + "Reaction 4NPHSFte is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 492\n", + "Reaction no. 498\n", + "Attempting to remove reaction: DM_sprm_c ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4506490000003396\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['SPRMS'], inactive_NC:['DM_sprm_c']\n", + "Reaction DM_sprm_c is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 491\n", + "Reaction no. 499\n", + "Attempting to remove reaction: 4NPHte ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1822989999991478\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['4NPHSULT'], inactive_NC:['EX_4nph_e', '4NPHSFte', '4NPHte', 'EX_4nphsf_e']\n", + "Reaction 4NPHte is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 490\n", + "Reaction no. 500\n", + "Attempting to remove reaction: PYDXtr ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1970369999999093\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['ENO', 'GLUt2m', 'PYDXDH', 'PGM'], inactive_NC:['EX_4pyrdx_e', 'EX_pydx_e', 'PYDXtr', '4PYRDX']\n", + "Reaction PYDXtr is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 489\n", + "Reaction no. 501\n", + "Attempting to remove reaction: PHEMEtm ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 488\n", + "Reaction no. 502\n", + "Attempting to remove reaction: ARACHt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4696610000000874\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['GLUt2m'], inactive_NC:['FATP4t', 'ARACHt']\n", + "Reaction ARACHt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 487\n", + "Reaction no. 503\n", + "Attempting to remove reaction: LGNCt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.430671999999504\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['GLUt2m', 'SERtN1'], inactive_NC:['FATP8t', 'LGNCt']\n", + "Reaction LGNCt is not in Z\n", + "1508\n", + "1508\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 486\n", + "Reaction no. 504\n", + "Attempting to remove reaction: CRVNCtr ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1975290000000314\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['GLUt2m', 'SERtN1'], inactive_NC:['FATP7t', 'CRVNCtr']\n", + "Reaction CRVNCtr is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 485\n", + "Reaction no. 505\n", + "Attempting to remove reaction: TETPENT3t ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1677580000005037\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['FACOAL245_2', 'DESAT24_1'], inactive_NC:['EX_tetpent3_e', 'ARTFR57', 'ARTFR55', 'TETPENT3t']\n", + "Reaction TETPENT3t is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 484\n", + "Reaction no. 506\n", + "Attempting to remove reaction: TTDCAtr ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 35 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6876329999995505\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 36 , inactive_C: ['THYMDt1', 'FACOAL140', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'NDPK5m', 'DCYTD', 'RNDR4'], inactive_NC:['EX_pi_e', 'EX_ttdca_e', 'HCO3_NAt', 'CEPTE', 'PA_HSter', 'TTDCAtr', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'PCHOLPr_hs', 'PGPP_hs', 'DUMPtn', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'NDP6']\n", + "Reaction TTDCAtr is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 483\n", + "Reaction no. 507\n", + "Attempting to remove reaction: ARTFR52 ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4115789999996196\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['FACOAL260'], inactive_NC:['HEXCt', 'ARTFR52', 'EX_hexc_e']\n", + "Reaction ARTFR52 is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 482\n", + "Reaction no. 508\n", + "Attempting to remove reaction: HEXCt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.195024999999987\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['NDPK5m', 'FACOAL260'], inactive_NC:['2HCO3_NAt', 'ARTFR52', 'EX_hexc_e', 'HEXCt']\n", + "Reaction HEXCt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 481\n", + "Reaction no. 509\n", + "Attempting to remove reaction: LNLCt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 19 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2740899999998874\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 20 , inactive_C: ['LNLCCPT2', 'DLNLCGCPT1', 'DESAT20_1', 'DESAT18_9', 'DLNLCGCRNt', 'FAOXC2031836m', 'LNLCCRNt', 'DLNLCGCPT2', 'LNLNCGCRNt', 'LNLNCGCPT1', 'LNLNCGCPT2', 'LNLCCPT1', 'FAEL183', 'FACOAL1821', 'FAOXC182806m'], inactive_NC:['ARTFR205', 'ARTFR210', 'EX_lnlc_e', 'LNLCt', 'ARTFR203']\n", + "Reaction LNLCt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 480\n", + "Reaction no. 510\n", + "Attempting to remove reaction: LNLNCAt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 27 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2288410000001022\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 28 , inactive_C: ['STRDNCCPT1', 'NKCC2t', 'FACOAL1832', 'LNLNCACPT2', 'FAEL205', 'FAEL184', 'EICOSTETCPT2', 'STRDNCCPT2', 'TMNDNCCRNt', 'LNLNCACRNt', 'EICOSTETCRNt', 'EICOSTETCPT1', 'FAOXC204184m', 'STRDNCCRNt', 'DESAT20_2', 'FAOXC183803m', 'LNLNCACPT1', 'TMNDNCCPT1', 'TMNDNCCPT2', 'DESAT18_10'], inactive_NC:['EX_pi_e', 'ARTFR211', 'EX_lnlnca_e', 'ARTFR208', 'ARTFR53', 'LNLNCAt', 'ARTFR202', 'ARTFR204']\n", + "Reaction LNLNCAt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 479\n", + "Reaction no. 511\n", + "Attempting to remove reaction: OCTAt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4363260000000082\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['FACOAL80'], inactive_NC:['EX_octa_e', '2HCO3_NAt', 'OCTAt']\n", + "Reaction OCTAt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 478\n", + "Reaction no. 512\n", + "Attempting to remove reaction: TETPENT6t ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.412015999999312\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['FACOAL245_1', 'NDPK5m', 'GDHm'], inactive_NC:['ARTFR54', 'TETPENT6t', 'EX_tetpent6_e']\n", + "Reaction TETPENT6t is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 477\n", + "Reaction no. 513\n", + "Attempting to remove reaction: TETTET6t ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2133460000004561\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['FACOAL244_1'], inactive_NC:['EX_pi_e', 'ARTFR56', 'TETTET6t', 'EX_tettet6_e']\n", + "Reaction TETTET6t is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 476\n", + "Reaction no. 514\n", + "Attempting to remove reaction: HPDCAt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2514900000005582\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['HPDCACRNCPT1', 'FACOAL170', 'FAOXC170m', 'HPDCACRNt', 'HPDCACRNCPT2'], inactive_NC:['EX_hpdca_e', 'HPDCAt']\n", + "Reaction HPDCAt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 475\n", + "Reaction no. 515\n", + "Attempting to remove reaction: PTDCAt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.369661000000633\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['PTDCACRNCPT1', 'PTDCACRNt', 'FACOAL150', 'PTDCACRNCPT2', 'FAOXC150m'], inactive_NC:['EX_ptdca_e', 'PTDCAt', '2HCO3_NAt']\n", + "Reaction PTDCAt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 474\n", + "Reaction no. 516\n", + "Attempting to remove reaction: GLXtp ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3151740000002974\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['GCALDD', 'FBA4', 'GLXO1', 'GLYCLTDy'], inactive_NC:['GLYCTO1p', 'GLYCLTtp', 'GLYtm', 'KHK2', 'GLXtp', 'EX_oxa_e']\n", + "Reaction GLXtp is not in Z\n", + "1508\n", + "1508\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 473\n", + "Reaction no. 517\n", + "Attempting to remove reaction: GLYCLTtp ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2261639999996987\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['GCALDD', 'NKCC2t', 'GLYCLTDy', 'FBA4', 'GLXO1'], inactive_NC:['GLYCTO1p', 'GLYCLTtp', 'KHK2', 'EX_oxa_e', 'GLXtp']\n", + "Reaction GLYCLTtp is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 472\n", + "Reaction no. 518\n", + "Attempting to remove reaction: EX_fe2_e ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.338090000000193\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['GLUt2m', 'CREATt4_2_r', 'SERtN1', 'DHAAt1r'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'EX_fe2_e', 'EX_fe3_e', 'FE3R2e', 'ASCBt4', 'GACMTRc']\n", + "Reaction EX_fe2_e is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 471\n", + "Reaction no. 519\n", + "Attempting to remove reaction: EX_fe3_e ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5064800000000105\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['DHAAt1r', 'LEUTAm'], inactive_NC:['EX_fe2_e', 'EX_fe3_e', 'FE3R2e', 'LEUt5m', '2HCO3_NAt', 'ASCBt4']\n", + "Reaction EX_fe3_e is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 470\n", + "Reaction no. 520\n", + "Attempting to remove reaction: RAI2 ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.187261000000035\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['RDH2a', 'SERtN1', 'PUNP1', 'LEUTAm'], inactive_NC:['RETFAt1', 'EX_retinol_9_cis_e', 'RETH1e', 'LEUt5m', '2HCO3_NAt', 'RAI2']\n", + "Reaction RAI2 is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 469\n", + "Reaction no. 521\n", + "Attempting to remove reaction: RETI1 ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2028390000004947\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['PIt8', 'RDH1a', 'TRIODTHYt2'], inactive_NC:['RETI1', 'RETH2e', 'EX_retinol_cis_11_e', 'RETFAt2', 'TRIODTHYt']\n", + "Reaction RETI1 is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 468\n", + "Reaction no. 522\n", + "Attempting to remove reaction: EX_biocyt_e ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 45 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5670110000000932\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 46 , inactive_C: ['DUTPDPn', 'PROt4', 'LEUTAm', 'PETOHMr_hs', 'SMS', 'PGPPT', 'DCYTD', 'RNDR4', 'THYMDt1', 'PSSA2_hs', 'SERtN1', 'HISt4', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'TRPt4', 'NTD3', 'NDPK6n'], inactive_NC:['EX_pi_e', 'CEPTE', 'PA_HSter', 'EX_his__L_e', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'GLCt4', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'PGPP_hs', 'EX_biocyt_e', 'DUMPtn', 'VBOF', 'LEUt5m', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'EX_pro__L_e', 'NDP6', 'HIStiDF']\n", + "Reaction EX_biocyt_e is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 467\n", + "Reaction no. 523\n", + "Attempting to remove reaction: XOLTRI25tc ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4240410000002157\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: [], inactive_NC:['EX_nh4_e', 'XOLTRI25te', 'P4507B11r', 'EX_xoltri25_e', 'XOLTRI25tc', 'CH25H']\n", + "Reaction XOLTRI25tc is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 466\n", + "Reaction no. 524\n", + "Attempting to remove reaction: ETOHt ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2192549999999756\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['ALCD2x', 'NKCC2t', 'ALCD2y', 'GLUt2m', 'PUNP1', 'CAT2p'], inactive_NC:['EX_etoh_e', 'ETOHMO', 'EX_h_e', 'ETOHt', 'ACALDtx', 'ETOHtx']\n", + "Reaction ETOHt is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 465\n", + "Reaction no. 525\n", + "Attempting to remove reaction: FALDtly ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 256 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7555959999999686\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 257 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'FPGS8', 'FPGS7', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'GGH_7THFl', 'CERT1rt', 'GGH_5THFl', 'SQLSr', 'FPGS4', 'C4STMO2r', 'MTHFCm', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'ACNAM9PL2', 'SOAT12', 'GGH_10FTHF6GLUl', 'GALUi', 'NDPK6n', 'FPGS9m', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'FPGS9', 'G6Pter', 'FPGS5m', 'GGH_10FTHF7GLUl', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'GASNASE2ly', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'FPGS6m', 'LSTO1r', 'GGH_7DHFl', 'DUTPDPn', 'FPGSm', 'AHEXASE2ly', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'FPGS3', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'FPGS3m', 'LSTO2r', 'FPGS7m', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'FPGS2m', 'HEX4', 'A_MANASEly', 'MEVK1x', 'SQLEr', 'SBPP1er', 'NTD3', 'FPGS8m', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'NKCC2t', 'C3STDH1r', 'GLDBRAN', 'GGH_5DHFl', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'FPGS6', 'GLGNS1', 'UGCG', 'FPGS4m', 'GGH_10FTHF5GLUl', 'PSSA2_hs', 'FPGS', 'DMATTx', 'DHCR242r', 'DHCRD2', 'FPGS5', 'FPGS2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'GGH_6DHFl', 'HSD17B9r', 'DHCR243r', 'GGH_6THFl'], inactive_NC:['H2O2tly', 'ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'THFtm', 'NDP7er', '7DHFtm', 'DHFtm', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', '6DHFtm', 'DHFtl', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', '10FTHFtl', '7THFtm', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'MANtly', 'DM_kdn_c', 'NADPtxu', '7DHFtl', '10FTHF7GLUtm', 'DM_dctp_m', 'EX_estrones_e', '6THFtl', 'DUDPtn', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'SARCStex', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'B_MANNASEly', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', '6THFtm', 'XOLTRI25tc', 'XOLTRI25te', 'SARCStm', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'SARDHm', 'KDNH', '10FTHF6GLUtm', '7THFtl', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'ENGASE2ly', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', '10FTHF5GLUtl', 'MEOHtly', 'THFtl', '6DHFtl', 'NADtru', 'HSD3B3r', 'DNDPt52m', '10FTHF5GLUtm', 'DCTPtn', '34HPPOR', 'ATPasel', '10FTHF7GLUtl', 'THMDt4', 'biomass_mac', 'PE_HSter', '5THFtl', 'EX_pe_hs_e', 'DNDPt54m', 'EX_sarcs_e', 'HAS1', 'O2ter', 'DOLPH_Ler', 'EX_n2m2nmasn_e', '5DHFtl', 'NADPtru', 'HAS2', '10FTHF6GLUtl', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'DM_dctp_n', 'AHCYStr', '5THFtm', 'GLUt7l', 'HAtly', 'PRDXl', 'EX_thymd_e', 'SPHK21c', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'N2M2NMASNtly', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'ACGAMtly', 'FALDtly', 'DM_Asn_X_Ser_Thr_l', 'NDP6', 'COAtp']\n", + "Reaction FALDtly is not in Z\n", + "1508\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1508\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 464\n", + "Reaction no. 526\n", + "Attempting to remove reaction: 5AOPtm ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Num. removed: 918 (119 core, 799 non-core); Num. remaining: 463\n", + "Reaction no. 527\n", + "Attempting to remove reaction: 25HVITD3tin_m ...\n", + "Initial PM reactions: 1508\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4028400000006513\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['25HVITD3tm', '25HVITD3tin_m']\n", + "Reaction 25HVITD3tin_m is not in Z\n", + "1508\n", + "1508\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1506\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 461\n", + "Reaction no. 528\n", + "Attempting to remove reaction: 25HVITD2tin_m ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4131870000001072\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['24_25VITD2Hm'], inactive_NC:['25HVITD2tm', 'EX_25hvitd2_e', '24_25DHVITD2tm', '25HVITD2tin', '24_25DHVITD2t', '25HVITD2tin_m', 'EX_2425dhvitd2_e']\n", + "Reaction 25HVITD2tin_m is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 460\n", + "Reaction no. 529\n", + "Attempting to remove reaction: 25HVITD2tm ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1508729999995921\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['NDPK5m', 'CREATt4_2_r', 'GLUt2m'], inactive_NC:['GACMTRc', '25HVITD2tm', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction 25HVITD2tm is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 459\n", + "Reaction no. 530\n", + "Attempting to remove reaction: 24_25DHVITD2tm ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1770430000005945\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['24_25VITD2Hm'], inactive_NC:['25HVITD2tin', 'EX_25hvitd2_e', '24_25DHVITD2tm', '24_25DHVITD2t', 'EX_2425dhvitd2_e']\n", + "Reaction 24_25DHVITD2tm is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 458\n", + "Reaction no. 531\n", + "Attempting to remove reaction: 24_25DHVITD3tm ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3932540000005247\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['24_25VITD3Hm'], inactive_NC:['24_25DHVITD3tm', 'EX_2425dhvitd3_e', '24_25DHVITD3t', 'EX_vitd3_e', 'VITD3Hm']\n", + "Reaction 24_25DHVITD3tm is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 457\n", + "Reaction no. 532\n", + "Attempting to remove reaction: EX_btn_e ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 43 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5252920000002632\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 44 , inactive_C: ['DUTPDPn', 'PROt4', 'PETOHMr_hs', 'SMS', 'PGPPT', 'PUNP1', 'DCYTD', 'RNDR4', 'THYMDt1', 'PSSA2_hs', 'HISt4', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'NDPK5m', 'TRPt4', 'NTD3', 'NDPK6n'], inactive_NC:['CEPTE', 'PA_HSter', 'EX_his__L_e', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'PGPP_hs', 'EX_biocyt_e', 'DUMPtn', 'VBOF', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', '2HCO3_NAt', 'EX_pro__L_e', 'NDP6', 'HIStiDF']\n", + "Reaction EX_btn_e is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 456\n", + "Reaction no. 533\n", + "Attempting to remove reaction: PPAtm ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.102162999999564\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PUNP1'], inactive_NC:['PPAtm', 'ACCOALm']\n", + "Reaction PPAtm is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 455\n", + "Reaction no. 534\n", + "Attempting to remove reaction: PPAtr ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1623020000006363\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['ACS2', 'GDHm', 'ACCOAL'], inactive_NC:['PPAtr', 'EX_ppa_e', 'PPAtm', 'ACCOALm']\n", + "Reaction PPAtr is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 454\n", + "Reaction no. 535\n", + "Attempting to remove reaction: MTRI ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 15 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1968909999995958\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 16 , inactive_C: ['SPMS', '2HBO', 'MTAP', 'SPRMS', 'BAMPPALDOX', '2HBt2', 'ADMDC'], inactive_NC:['DM_sprm_c', '13DAMPPOX', 'UNK2', 'UNK3', 'SPMDOX', 'MDRPD', 'EX_2hb_e', 'MTRI', 'DKMPPD']\n", + "Reaction MTRI is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 453\n", + "Reaction no. 536\n", + "Attempting to remove reaction: 7DHFtm ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4017409999996744\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['FPGS6m', 'SERtN1'], inactive_NC:['EX_pi_e', '7DHFtm']\n", + "Reaction 7DHFtm is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 452\n", + "Reaction no. 537\n", + "Attempting to remove reaction: 10FTHF7GLUtm ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.40089799999987\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['FPGS9m'], inactive_NC:['10FTHF7GLUtm']\n", + "Reaction 10FTHF7GLUtm is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 451\n", + "Reaction no. 538\n", + "Attempting to remove reaction: 7THFtm ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.208016999999927\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['FPGS3m'], inactive_NC:['7THFtm', 'EX_pi_e']\n", + "Reaction 7THFtm is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 450\n", + "Reaction no. 539\n", + "Attempting to remove reaction: EX_tyr__L_e ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1389599999993152\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['TYRt4'], inactive_NC:['EX_tyr__L_e']\n", + "Reaction EX_tyr__L_e is not in Z\n", + "1506\n", + "1506\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 449\n", + "Reaction no. 540\n", + "Attempting to remove reaction: EX_pro__L_e ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 42 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5285930000000008\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 43 , inactive_C: ['DUTPDPn', 'PROt4', 'PETOHMr_hs', 'SMS', 'PGPPT', 'PUNP1', 'DCYTD', 'RNDR4', 'THYMDt1', 'GDHm', 'PSSA2_hs', 'HISt4', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'TRPt4', 'NTD3', 'NDPK6n'], inactive_NC:['CEPTE', 'PA_HSter', 'EX_his__L_e', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'PGPP_hs', 'EX_biocyt_e', 'DUMPtn', 'VBOF', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'EX_pro__L_e', 'NDP6', 'HIStiDF']\n", + "Reaction EX_pro__L_e is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 920 (119 core, 801 non-core); Num. remaining: 448\n", + "Reaction no. 541\n", + "Attempting to remove reaction: MI14Ptn ...\n", + "Initial PM reactions: 1506\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4035239999993792\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['MI14Ptn', 'PI4PLCn']\n", + "Reaction MI14Ptn is not in Z\n", + "1506\n", + "1506\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1504\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 447\n", + "Reaction no. 542\n", + "Attempting to remove reaction: EX_trp__L_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 42 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4920249999995576\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 43 , inactive_C: ['THYMDt1', 'NKCC2t', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'PROt4', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'HISt4', 'DCYTD', 'RNDR4', 'TRPt4'], inactive_NC:['CEPTE', 'PA_HSter', 'EX_his__L_e', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'PGPP_hs', 'EX_biocyt_e', 'DUMPtn', 'VBOF', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', '2HCO3_NAt', 'EX_pro__L_e', 'NDP6', 'HIStiDF']\n", + "Reaction EX_trp__L_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 446\n", + "Reaction no. 543\n", + "Attempting to remove reaction: EX_his__L_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 42 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2366549999997005\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 43 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'PROt4', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'NDPK5m', 'HISt4', 'DCYTD', 'RNDR4', 'TRPt4'], inactive_NC:['CEPTE', 'PA_HSter', 'EX_his__L_e', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'GLCt4', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'PGPP_hs', 'EX_biocyt_e', 'DUMPtn', 'VBOF', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'EX_pro__L_e', 'NDP6', 'HIStiDF']\n", + "Reaction EX_his__L_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 445\n", + "Reaction no. 544\n", + "Attempting to remove reaction: EX_creat_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.200736999999208\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['PIt8', 'CREATt4_2_r'], inactive_NC:['GACMTRc', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction EX_creat_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 444\n", + "Reaction no. 545\n", + "Attempting to remove reaction: EX_ocdca_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 33 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5080550000002404\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 34 , inactive_C: ['THYMDt1', 'DUTPDPn', 'GDHm', 'PSSA2_hs', 'FACOAL161', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'FACOAL180', 'FATP3t', 'DCYTD', 'RNDR4'], inactive_NC:['THMDt4', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'PEFLIP', 'EX_ocdca_e', 'NDP6', 'AHCYStr']\n", + "Reaction EX_ocdca_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 443\n", + "Reaction no. 546\n", + "Attempting to remove reaction: EX_ocdcea_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 33 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.54214200000024\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 34 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'FACOAL181', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'FATP2t', 'DGAT', 'DCYTD', 'RNDR4'], inactive_NC:['EX_pi_e', 'THMDt4', 'NDP6', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'PEFLIP', 'EX_ocdcea_e', 'AHCYStr']\n", + "Reaction EX_ocdcea_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 442\n", + "Reaction no. 547\n", + "Attempting to remove reaction: EX_phe__L_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 54 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2525660000001153\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 55 , inactive_C: ['DUTPDPn', 'PEAMNO', 'PROt4', 'PETOHMr_hs', 'SMS', 'PGPPT', 'PUNP1', 'DCYTD', 'RNDR4', 'PHEt4', 'THYMDt1', 'PSSA2_hs', 'ALDD19xr', 'SERtN1', 'HISt4', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'NDPK5m', 'ALDD19x_P', 'TRPt4', 'NTD3', 'NDPK6n'], inactive_NC:['EX_pheacgln_e', 'CEPTE', 'PA_HSter', 'EX_his__L_e', 'AHCYStr', 'NDP6', 'PHETHPTOX2', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'PACCOAL', 'PHEACGLNt', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'EX_phe__L_e', 'PGPP_hs', 'EX_biocyt_e', 'DUMPtn', 'VBOF', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'PHACCOAGLNAC', 'EX_pro__L_e', 'PHYCBOXL', 'HIStiDF']\n", + "Reaction EX_phe__L_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 441\n", + "Reaction no. 548\n", + "Attempting to remove reaction: EX_val__L_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 56 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5203270000001794\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 57 , inactive_C: ['DUTPDPn', 'PROt4', 'PETOHMr_hs', 'SMS', 'PGPPT', 'HIBDm', 'DCYTD', 'ECOAH12m', 'RNDR4', 'THYMDt1', 'GDHm', 'PSSA2_hs', 'HISt4', 'VALt4', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'TRPt4', 'NTD3', 'OIVD2m', 'ACOAD9m', 'NDPK6n', 'VALTAim'], inactive_NC:['MMSAD1m', 'CEPTE', 'PA_HSter', 'EX_his__L_e', 'AHCYStr', 'EX_val__L_e', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'PGPP_hs', 'EX_biocyt_e', 'DUMPtn', '3AIBtm', 'VBOF', '3AIBTm', 'PEFLIP', '3AIBt', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'MMTSADm', 'EX_3aib_e', 'VALt5m', '3HBCOAHLm', 'EX_pro__L_e', 'NDP6', 'HIStiDF']\n", + "Reaction EX_val__L_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 440\n", + "Reaction no. 549\n", + "Attempting to remove reaction: HDD2COAtx ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.398190999999315\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['NKCC2t', 'FAOXC161802m', 'C161CPT22', 'SERtN1', 'C161CRN2t', 'C161CPT12'], inactive_NC:['ACOAO7p', 'HDD2COAtx', 'ARTFR61', 'RTOT6', 'PMTCOAtx']\n", + "Reaction HDD2COAtx is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 439\n", + "Reaction no. 550\n", + "Attempting to remove reaction: EX_dad_2_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 43 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.330354000000625\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 44 , inactive_C: ['DUTPDPn', 'PETOHMr_hs', 'SMS', 'PGPPT', 'PUNP6', 'DCYTD', 'RNDR4', 'THYMDt1', 'PSSA2_hs', 'CREATt4_2_r', 'DADA', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'NTD3', 'DADAe', 'NDPK6n', 'INSt'], inactive_NC:['DADNt4', 'DINt', 'DRBK', 'CEPTE', 'PA_HSter', 'GACMTRc', 'AHCYStr', 'EX_creat_e', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'PCHOLPr_hs', 'PGPP_hs', 'DUMPtn', 'PEFLIP', 'EX_dad_2_e', 'THMDt4', 'GLYAMDTRc', 'biomass_mac', 'PE_HSter', 'DRPA', 'EX_pe_hs_e', '2DR1PP', 'NDP6']\n", + "Reaction EX_dad_2_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 438\n", + "Reaction no. 551\n", + "Attempting to remove reaction: EX_adp_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2197320000004765\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['ATPH2e', 'SERtN1'], inactive_NC:['EX_adp_e']\n", + "Reaction EX_adp_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 437\n", + "Reaction no. 552\n", + "Attempting to remove reaction: EX_atp_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4882520000001023\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['MTHFD2m', 'ATPH1e', 'GLUt2m', 'NDPK5m'], inactive_NC:['EX_atp_e', 'EX_h_e', '2HCO3_NAt']\n", + "Reaction EX_atp_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 436\n", + "Reaction no. 553\n", + "Attempting to remove reaction: EX_idp_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.411844000000201\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['NDP10ex', 'GDHm'], inactive_NC:['2HCO3_NAt', 'EX_idp_e', 'EX_imp_e']\n", + "Reaction EX_idp_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 435\n", + "Reaction no. 554\n", + "Attempting to remove reaction: EX_imp_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1391640000001644\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['NDP10ex', 'PUNP1'], inactive_NC:['EX_idp_e', 'EX_imp_e']\n", + "Reaction EX_imp_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 434\n", + "Reaction no. 555\n", + "Attempting to remove reaction: EX_utp_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.117156999999679\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['NKCC2t', 'NDP7ex', 'NDP8ex', 'SERtN1', 'NDPK5m', 'PUNP1', 'NTD2e'], inactive_NC:['EX_pi_e', 'EX_utp_e', 'URIt5']\n", + "Reaction EX_utp_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 433\n", + "Reaction no. 556\n", + "Attempting to remove reaction: EX_gtp_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4468370000004143\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['NTP3e', 'NDP3ex', 'NTD9e'], inactive_NC:['GSNt4', 'EX_gtp_e']\n", + "Reaction EX_gtp_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 432\n", + "Reaction no. 557\n", + "Attempting to remove reaction: EX_pchol_hs_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.438836000000265\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['PLA2_2e', 'NKCC2t', 'PUNP1', 'GDHm'], inactive_NC:['EX_pchol_hs_e', 'EX_lpchol_hs_e', 'HCO3_NAt']\n", + "Reaction EX_pchol_hs_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 431\n", + "Reaction no. 558\n", + "Attempting to remove reaction: EX_lpchol_hs_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1407719999997425\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PLA2_2e'], inactive_NC:['EX_pchol_hs_e', 'EX_lpchol_hs_e']\n", + "Reaction EX_lpchol_hs_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 430\n", + "Reaction no. 559\n", + "Attempting to remove reaction: EX_Rtotal2_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 21 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1626070000002073\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 22 , inactive_C: ['PUNP5', 'CREATt4_2_r', 'RDH2a', 'PLA2_2e', 'RDH1a'], inactive_NC:['BCDO', 'RETFAt1', 'EX_creat_e', 'EX_retinol_9_cis_e', 'EX_pchol_hs_e', 'GLYAMDTRc', 'EX_lpchol_hs_e', 'RETH1e', 'CAROtr', 'RETI1', 'RETH2e', 'EX_retinol_cis_11_e', 'EX_Rtotal2_e', 'EX_caro_e', 'GACMTRc', 'RAI2', 'RETFAt2']\n", + "Reaction EX_Rtotal2_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 429\n", + "Reaction no. 560\n", + "Attempting to remove reaction: PAIL_HStn ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1687599999995655\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['DAGKn_hs', 'GDHm'], inactive_NC:['PA_HStn', 'MI1P_Dtn', 'PAIL_HStn', 'PIPLCn']\n", + "Reaction PAIL_HStn is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 428\n", + "Reaction no. 561\n", + "Attempting to remove reaction: DCSPTN1COAtx ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3250110000008135\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['DCSPTN1CPT1', 'FAOXC2251836m', 'DCSPTN1CPT2', 'XANDp', 'DCSPTN1CRNt', 'FAOXC2252053m'], inactive_NC:['ADRNCOAtx', 'ARTFR212', 'DCSPTN1COAtx', 'DESAT22_1p']\n", + "Reaction DCSPTN1COAtx is not in Z\n", + "1504\n", + "1504\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 427\n", + "Reaction no. 562\n", + "Attempting to remove reaction: 5THFtm ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3530709999995452\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['SERtN1', 'PUNP1', 'GDHm'], inactive_NC:['5THFtm', '2HCO3_NAt']\n", + "Reaction 5THFtm is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 426\n", + "Reaction no. 563\n", + "Attempting to remove reaction: 10FTHF5GLUtm ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1661960000001272\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['ENO', 'PGM'], inactive_NC:['10FTHF5GLUtm']\n", + "Reaction 10FTHF5GLUtm is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 425\n", + "Reaction no. 564\n", + "Attempting to remove reaction: 6THFtm ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2431169999999838\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['GLUt2m', 'SERtN1'], inactive_NC:['EX_pi_e', '6THFtm']\n", + "Reaction 6THFtm is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 424\n", + "Reaction no. 565\n", + "Attempting to remove reaction: 10FTHF6GLUtm ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4287029999995866\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CREATt4_2_r', 'GLUt2m'], inactive_NC:['10FTHF6GLUtm', 'GACMTRc', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction 10FTHF6GLUtm is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 423\n", + "Reaction no. 566\n", + "Attempting to remove reaction: 6DHFtm ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.468217999999979\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['NDPK5m'], inactive_NC:['6DHFtm', 'EX_pi_e', 'HCO3_NAt']\n", + "Reaction 6DHFtm is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 422\n", + "Reaction no. 567\n", + "Attempting to remove reaction: ACALDtm ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1062569999994594\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['ALDD2xm', 'PUNP1'], inactive_NC:['ACALDtm', 'ACSm']\n", + "Reaction ACALDtm is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 421\n", + "Reaction no. 568\n", + "Attempting to remove reaction: ADRNCOAtx ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2087620000002062\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['DCSPTN1CPT1', 'FAOXC2251836m', 'DCSPTN1CPT2', 'XANDp', 'PUNP1', 'DCSPTN1CRNt', 'FAOXC2252053m'], inactive_NC:['ADRNCOAtx', 'ARTFR212', 'NH4t3r', 'DESAT22_1p', 'DCSPTN1COAtx']\n", + "Reaction ADRNCOAtx is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 420\n", + "Reaction no. 569\n", + "Attempting to remove reaction: PPPG9tm ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 419\n", + "Reaction no. 570\n", + "Attempting to remove reaction: PA_HSter ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 31 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6454359999997905\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 32 , inactive_C: ['THYMDt1', 'DUTPDPn', 'GDHm', 'PSSA2_hs', 'FACOAL161', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'NDPK5m', 'DCYTD', 'RNDR4'], inactive_NC:['THMDt4', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'PEFLIP', 'NDP6', 'AHCYStr']\n", + "Reaction PA_HSter is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 418\n", + "Reaction no. 571\n", + "Attempting to remove reaction: DGSNtm ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.400814999999966\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['NTD8', 'DGNSKm'], inactive_NC:['EX_pi_e', 'EX_nh4_e', 'DGK2m', '2HCO3_NAt', 'DGSNtm']\n", + "Reaction DGSNtm is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 417\n", + "Reaction no. 572\n", + "Attempting to remove reaction: ARTFR13 ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 106 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7465349999993123\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 107 , inactive_C: ['RTOTAL3CRNt', 'DUTPDPn', 'DESAT24_1', 'RTOTAL3CRNCPT2', 'PETOHMr_hs', 'SMS', 'PNTK', 'PGPPT', 'FAEL205', 'PUNP1', 'DCYTD', 'RNDR4', 'THYMDt1', 'FACOAL241', 'PPNCL3', 'PSSA2_hs', 'FACOAL245_2', 'RTOTAL2CRNCPT1', 'PPCDC', 'RTOTAL2CRNt', 'DPCOAK', 'FACOAL161', 'FACOAL244_1', 'RTOTAL2CRNCPT2', 'TMDS', 'FACOAL260', 'PETHCT', 'FACOAL245_1', 'DGAT', 'RDH1a', 'NTD3', 'SOAT12', 'RDH2a', 'NDPK6n', 'RTOTAL3CRNCPT1'], inactive_NC:['ARTFR54', 'EX_hexc_e', 'EX_retinol_9_cis_e', 'EX_tetpent3_e', 'RETH1e', 'ARTFR55', 'CEPTE', 'PA_HSter', 'TETPENT6t', 'RTOT2', 'ARTFR210', 'RETH2e', 'ARTFR209', 'RETFAt2', 'ARTFR202', 'AHCYStr', 'NDP6', 'EX_tetpent6_e', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_pnto__R_e', 'EX_tettet6_e', 'ARTFR46', 'ARTFR45', 'ARTFR44', 'ARTFR205', 'PCHOLPr_hs', 'ARTFR52', 'TETTET6t', 'PGPP_hs', 'RTOT_3', 'EX_caro_e', 'ARTFR32', 'RTOT5', 'EX_nrvnc_e', 'RAI2', 'BCDO', 'ARTFR203', 'RETFAt1', 'ARTFR57', 'ARTFR31', 'DUMPtn', 'ARTFR208', 'CAROtr', 'EX_retinol_cis_11_e', 'ARTFR13', 'PEFLIP', 'HEXCt', 'ARTFR34', 'ARTFR53', 'ARTFR56', 'ARTFR33', 'ARTFR204', 'ARTFR42', 'THMDt4', 'ARTFR211', 'biomass_mac', 'PNTOt5', 'PE_HSter', 'ARTFR212', 'EX_pe_hs_e', 'ARTPLM2m', 'TETPENT3t', 'RTOT3', 'RETI1', 'ARTFR206', 'ARTPLM3m', 'ARTFR43', 'FATP9t', 'RTOT_2']\n", + "Reaction ARTFR13 is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 416\n", + "Reaction no. 573\n", + "Attempting to remove reaction: EX_cmp_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1859560000002602\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['NTD4e', 'LEUTAm'], inactive_NC:['EX_cmp_e', 'LEUt5m', 'CYTDt4', 'CYTDt5']\n", + "Reaction EX_cmp_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 415\n", + "Reaction no. 574\n", + "Attempting to remove reaction: EX_estrones_e ...\n", + "Initial PM reactions: 1504\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1131759999998394\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['HSD17B7r', 'NKCC2t', 'SERtN1', 'HSD17B8r'], inactive_NC:['P4501B1r', 'HESTRATRIOLtr', 'EX_hestratriol_e', '2HCO3_NAt', 'ESTRONESt2', 'ESTRONEtr', 'HESTRATRIOLte', 'EX_estrones_e']\n", + "Reaction EX_estrones_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 414\n", + "Reaction no. 575\n", + "Attempting to remove reaction: EX_strch1_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.513173999999708\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['AMY1e', 'MALT', 'PUNP1'], inactive_NC:['MALTe', 'EX_strch1_e', 'MALTt1r', 'O16G2e']\n", + "Reaction EX_strch1_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 413\n", + "Reaction no. 576\n", + "Attempting to remove reaction: GLYtm ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 412\n", + "Reaction no. 577\n", + "Attempting to remove reaction: XOLESTte ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4342310000001817\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['SOAT12', 'SOAT11', 'LEUTAm'], inactive_NC:['LEUt5m', 'EX_xolest_hs_e', 'XOLESTte']\n", + "Reaction XOLESTte is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 411\n", + "Reaction no. 578\n", + "Attempting to remove reaction: EX_10fthf_e ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1484159999999974\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['GGH_10FTHF5GLUe', 'GGH_10FTHF6GLUe', 'CREATt4_2_r', 'PUNP1', 'NDPK5m', 'GGH_10FTHF7GLUe'], inactive_NC:['EX_10fthf7glu_e', 'EX_creat_e', 'EX_10fthf_e', 'GLYAMDTRc', 'GACMTRc']\n", + "Reaction EX_10fthf_e is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 922 (119 core, 803 non-core); Num. remaining: 410\n", + "Reaction no. 579\n", + "Attempting to remove reaction: RTOT3 ...\n", + "Initial PM reactions: 1504\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2064110000001165\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['ARTFR31', 'ARTFR32', 'ARTFR34', 'ARTFR33', 'RTOT3']\n", + "Reaction RTOT3 is not in Z\n", + "1504\n", + "1504\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1499\n", + "Num. removed: 927 (119 core, 808 non-core); Num. remaining: 405\n", + "Reaction no. 580\n", + "Attempting to remove reaction: RTOT4 ...\n", + "Initial PM reactions: 1499\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3995479999994132\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['2HBO', 'LEUTAm', 'SERtN1', 'NDPK5m', '2HBt2'], inactive_NC:['LEUt5m', 'RTOT4', 'EX_2hb_e']\n", + "Reaction RTOT4 is not in Z\n", + "1499\n", + "1499\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 927 (119 core, 808 non-core); Num. remaining: 404\n", + "Reaction no. 581\n", + "Attempting to remove reaction: RTOT5 ...\n", + "Initial PM reactions: 1499\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 20 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4204069999996136\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 21 , inactive_C: ['DESAT24_1', 'FACOAL244_1', 'FACOAL260', 'FACOAL245_2', 'FACOAL245_1', 'GLUt2m'], inactive_NC:['ARTFR57', 'EX_hexc_e', 'ARTFR54', 'EX_tetpent6_e', 'EX_tetpent3_e', 'ARTFR55', 'TETPENT6t', 'EX_tettet6_e', 'TETPENT3t', 'ARTFR52', 'TETTET6t', 'HEXCt', 'RTOT5', 'ARTFR56', 'ARTFR53']\n", + "Reaction RTOT5 is not in Z\n", + "1499\n", + "1499\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 927 (119 core, 808 non-core); Num. remaining: 403\n", + "Reaction no. 582\n", + "Attempting to remove reaction: RTOT6 ...\n", + "Initial PM reactions: 1499\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2049450000004072\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['ARTFR61', '2HCO3_NAt', 'RTOT6']\n", + "Reaction RTOT6 is not in Z\n", + "1499\n", + "1499\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1496\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 400\n", + "Reaction no. 583\n", + "Attempting to remove reaction: EX_h2o2_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1766710000001694\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['GTHPe'], inactive_NC:['EX_gthrd_e', 'EX_h2o2_e', 'EX_gthox_e']\n", + "Reaction EX_h2o2_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 399\n", + "Reaction no. 584\n", + "Attempting to remove reaction: EX_10fthf7glu_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4295269999993252\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GGH_10FTHF5GLUe', 'GGH_10FTHF6GLUe', 'GGH_10FTHF7GLUe'], inactive_NC:['EX_10fthf7glu_e', 'EX_10fthf_e']\n", + "Reaction EX_10fthf7glu_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 398\n", + "Reaction no. 585\n", + "Attempting to remove reaction: EX_7dhf_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4291510000002745\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['GGH_6DHFe', 'CREATt4_2_r', 'HCO3_CLt', 'GGH_7DHFe', 'GGH_5DHFe'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'NH4t3r', 'EX_dhf_e', 'EX_7dhf_e', 'GACMTRc']\n", + "Reaction EX_7dhf_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 397\n", + "Reaction no. 586\n", + "Attempting to remove reaction: EX_7thf_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1817900000005466\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['CREATt4_2_r', 'GGH_5THFe', 'GGH_6THFe', 'GGH_7THFe', 'HCO3_CLt'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'NH4t3r', 'EX_7thf_e', 'EX_thf_e', 'GACMTRc']\n", + "Reaction EX_7thf_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 396\n", + "Reaction no. 587\n", + "Attempting to remove reaction: EX_dhf_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.411645000000135\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['GGH_5DHFe', 'GGH_6DHFe', 'GGH_7DHFe'], inactive_NC:['EX_pi_e', 'EX_7dhf_e', 'EX_dhf_e', 'HCO3_NAt']\n", + "Reaction EX_dhf_e is not in Z\n", + "1496\n", + "1496\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 395\n", + "Reaction no. 588\n", + "Attempting to remove reaction: EX_gthox_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4230500000003303\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['GTHPe'], inactive_NC:['EX_gthrd_e', 'EX_h2o2_e', 'EX_gthox_e']\n", + "Reaction EX_gthox_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 394\n", + "Reaction no. 589\n", + "Attempting to remove reaction: EX_thf_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.186225999999806\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['GGH_6THFe', 'GGH_7THFe', 'GGH_5THFe'], inactive_NC:['NAHCO3_HCLt', 'EX_thf_e', 'NH4t3r', 'EX_7thf_e']\n", + "Reaction EX_thf_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 393\n", + "Reaction no. 590\n", + "Attempting to remove reaction: EX_gthrd_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1615990000000238\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['GTHPe'], inactive_NC:['EX_gthrd_e', 'EX_h2o2_e', 'EX_gthox_e']\n", + "Reaction EX_gthrd_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 392\n", + "Reaction no. 591\n", + "Attempting to remove reaction: DINt ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1825589999998556\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['DADAe', 'SERtN1'], inactive_NC:['DINt']\n", + "Reaction DINt is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 391\n", + "Reaction no. 592\n", + "Attempting to remove reaction: PMTCOAtx ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4370989999997619\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['NKCC2t', 'FAOXC161802m', 'C161CPT22', 'SERtN1', 'MTHFD2m', 'PUNP1', 'C161CRN2t', 'C161CPT12'], inactive_NC:['ACOAO7p', 'HDD2COAtx', 'PMTCOAtx']\n", + "Reaction PMTCOAtx is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 390\n", + "Reaction no. 593\n", + "Attempting to remove reaction: EX_cysi__L_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4289449999996577\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['NKCC2t', 'CYSTGLUex'], inactive_NC:['CYSTSERex', 'EX_cysi__L_e', 'CYSGLTH']\n", + "Reaction EX_cysi__L_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 389\n", + "Reaction no. 594\n", + "Attempting to remove reaction: EX_ksi_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2115579999999682\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['FUCASE2e'], inactive_NC:['EX_ksi_e', 'EX_ksi_deg1_e']\n", + "Reaction EX_ksi_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 388\n", + "Reaction no. 595\n", + "Attempting to remove reaction: EX_ksi_deg1_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4503230000000258\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['FUCASE2e', 'CREATt4_2_r'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'EX_ksi_deg1_e', 'EX_ksi_e', 'NAHCO3_HCLt', 'GACMTRc']\n", + "Reaction EX_ksi_deg1_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 387\n", + "Reaction no. 596\n", + "Attempting to remove reaction: EX_s2l2fn2m2masn_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 184 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.034469999999601\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 185 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'SOAT12', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'NDPK5m', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'MEVK1x', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'GLCt4', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', 'DCTPtn', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'DM_dctp_n', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'NDP6', 'COAtp']\n", + "Reaction EX_s2l2fn2m2masn_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 386\n", + "Reaction no. 597\n", + "Attempting to remove reaction: DADNt4 ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 34 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2964820000006512\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 35 , inactive_C: ['THYMDt1', 'DUTPDPn', 'GDHm', 'PSSA2_hs', 'FACOAL161', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'DADA', 'SMS', 'PGPPT', 'NDPK6n', 'PUNP1', 'DGAT', 'NDPK5m', 'DCYTD', 'RNDR4'], inactive_NC:['THMDt4', 'DADNt4', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'PEFLIP', 'NDP6', 'AHCYStr']\n", + "Reaction DADNt4 is not in Z\n", + "1496\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1496\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 930 (119 core, 811 non-core); Num. remaining: 385\n", + "Reaction no. 598\n", + "Attempting to remove reaction: EX_for_e ...\n", + "Initial PM reactions: 1496\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1703729999999268\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['CLFORtex2', 'CLFORtex', 'EX_for_e']\n", + "Reaction EX_for_e is not in Z\n", + "1496\n", + "1496\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1493\n", + "Num. removed: 933 (119 core, 814 non-core); Num. remaining: 383\n", + "Reaction no. 599\n", + "Attempting to remove reaction: CHSTEROLt3 ...\n", + "Initial PM reactions: 1493\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 37 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4320809999999256\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 38 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'SOAT12', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'SERtN1', 'DGAT', 'DCYTD', 'RNDR4', 'SOAT11'], inactive_NC:['EX_pi_e', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'PCHOLPr_hs', 'PGPP_hs', 'DUMPtn', 'CHSTEROLt3', 'PEFLIP', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'NDP6']\n", + "Reaction CHSTEROLt3 is not in Z\n", + "1493\n", + "1493\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 933 (119 core, 814 non-core); Num. remaining: 382\n", + "Reaction no. 600\n", + "Attempting to remove reaction: C204CRNt ...\n", + "Initial PM reactions: 1493\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4696789999998146\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['C204CPT2', 'C204CPT1'], inactive_NC:['C204CRNt']\n", + "Reaction C204CRNt is not in Z\n", + "1493\n", + "1493\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 933 (119 core, 814 non-core); Num. remaining: 381\n", + "Reaction no. 601\n", + "Attempting to remove reaction: PCREATtmdiffir ...\n", + "Initial PM reactions: 1493\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4459130000004734\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['CK', 'CKc'], inactive_NC:['PCREATtmdiffir', 'CREATtmdiffir']\n", + "Reaction PCREATtmdiffir is not in Z\n", + "1493\n", + "1493\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 933 (119 core, 814 non-core); Num. remaining: 380\n", + "Reaction no. 602\n", + "Attempting to remove reaction: 3AIBtm ...\n", + "Initial PM reactions: 1493\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1308060000001205\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['NDPK5m'], inactive_NC:['3AIBTm', 'EX_3aib_e', '3AIBt', '3AIBtm']\n", + "Reaction 3AIBtm is not in Z\n", + "1493\n", + "1493\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 933 (119 core, 814 non-core); Num. remaining: 379\n", + "Reaction no. 603\n", + "Attempting to remove reaction: AHCYStr ...\n", + "Initial PM reactions: 1493\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 37 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3924900000001799\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 38 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'CREATt4_2_r', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'SERtN1', 'PUNP1', 'DGAT', 'HCO3_CLt', 'DCYTD', 'RNDR4'], inactive_NC:['EX_pi_e', 'CEPTE', 'PA_HSter', 'GACMTRc', 'AHCYStr', 'EX_creat_e', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'PCHOLPr_hs', 'PGPP_hs', 'DUMPtn', 'PEFLIP', 'THMDt4', 'GLYAMDTRc', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'NDP6']\n", + "Reaction AHCYStr is not in Z\n", + "1493\n", + "1493\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 933 (119 core, 814 non-core); Num. remaining: 378\n", + "Reaction no. 604\n", + "Attempting to remove reaction: O2Stx ...\n", + "Initial PM reactions: 1493\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 49 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4820300000001225\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 50 , inactive_C: ['GCALDD', 'CATp', 'FAOXC161802m', 'FBA4', 'C161CPT22', 'XAOx', 'PUNP1', 'ALAR', 'GLYCLTDy', 'DCSPTN1CPT1', 'SERtN1', 'CAT2p', 'PYRt2p', 'PUNP7', 'DCSPTN1CPT2', 'C161CRN2t', 'C161CPT12', 'FAOXC2252053m', 'GLXO1', 'NTD10', 'FAOXC2251836m', 'XAO2x', 'SPODMx', 'XANDp', 'DCSPTN1CRNt'], inactive_NC:['H2Otp', 'GLYCTO1p', 'PMTCOAtx', 'DESAT22_1p', 'ETOHtx', 'EX_oxa_e', 'GLXtp', 'GUAD', 'DCSPTN1COAtx', 'URATEt', 'DALAxt', 'ADRNCOAtx', 'GLYCLTtp', 'DALAOXx', 'ACOAO7p', 'HDD2COAtx', 'URATEtx', 'HXANtx', 'NH4tp', 'XANtx', 'O2Stx', 'ARTFR212', 'EX_urate_e', 'KHK2', 'ACALDtx']\n", + "Reaction O2Stx is not in Z\n", + "1493\n", + "1493\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 933 (119 core, 814 non-core); Num. remaining: 377\n", + "Reaction no. 605\n", + "Attempting to remove reaction: AMETr ...\n", + "Initial PM reactions: 1493\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 33 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.684240999999929\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 34 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'CREATt4_2_r', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'DCYTD', 'RNDR4'], inactive_NC:['CEPTE', 'PA_HSter', 'GACMTRc', 'AHCYStr', 'EX_creat_e', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'PCHOLPr_hs', 'PGPP_hs', 'DUMPtn', 'PEFLIP', 'THMDt4', 'GLYAMDTRc', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'NDP6']\n", + "Reaction AMETr is not in Z\n", + "1493\n", + "1493\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 933 (119 core, 814 non-core); Num. remaining: 376\n", + "Reaction no. 606\n", + "Attempting to remove reaction: RTOT2 ...\n", + "Initial PM reactions: 1493\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1355410000005577\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['CREATt4_2_r'], inactive_NC:['RTOT2', 'GACMTRc', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction RTOT2 is not in Z\n", + "1493\n", + "1493\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 933 (119 core, 814 non-core); Num. remaining: 375\n", + "Reaction no. 607\n", + "Attempting to remove reaction: RTOT_2 ...\n", + "Initial PM reactions: 1493\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 47 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3537340000002587\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 48 , inactive_C: ['DUTPDPn', 'PETOHMr_hs', 'SMS', 'PGPPT', 'DCYTD', 'RNDR4', 'THYMDt1', 'PSSA2_hs', 'RTOTAL2CRNCPT1', 'RTOTAL2CRNt', 'FACOAL161', 'RTOTAL2CRNCPT2', 'TMDS', 'PETHCT', 'DGAT', 'RDH1a', 'NTD3', 'RDH2a', 'NDPK6n'], inactive_NC:['EX_retinol_9_cis_e', 'RETH1e', 'CEPTE', 'PA_HSter', 'RETH2e', 'RETFAt2', 'AHCYStr', 'NDP6', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'PCHOLPr_hs', 'PGPP_hs', 'EX_caro_e', 'RAI2', 'BCDO', 'RETFAt1', 'DUMPtn', 'CAROtr', 'EX_retinol_cis_11_e', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'ARTPLM2m', 'RETI1', 'RTOT_2']\n", + "Reaction RTOT_2 is not in Z\n", + "1493\n", + "1493\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 933 (119 core, 814 non-core); Num. remaining: 374\n", + "Reaction no. 608\n", + "Attempting to remove reaction: RTOT1 ...\n", + "Initial PM reactions: 1493\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.424724000000424\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['EX_pi_e', 'RTOT1']\n", + "Reaction RTOT1 is not in Z\n", + "1493\n", + "1493\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 933 (119 core, 814 non-core); Num. remaining: 373\n", + "Reaction no. 609\n", + "Attempting to remove reaction: ARTFR11 ...\n", + "Initial PM reactions: 1493\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4123369999997522\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['ARTFR11']\n", + "Reaction ARTFR11 is not in Z\n", + "1493\n", + "1493\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1492\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 372\n", + "Reaction no. 610\n", + "Attempting to remove reaction: DM_dctp_n ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2517669999997452\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['LEUTAm'], inactive_NC:['DCTPtn', 'DM_dctp_n', 'LEUt5m']\n", + "Reaction DM_dctp_n is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 371\n", + "Reaction no. 611\n", + "Attempting to remove reaction: SPHS1Ptr ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1903480000000854\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['SBPP3er'], inactive_NC:['SPHS1Ptr', 'SPHK21c', 'SPHINGStr']\n", + "Reaction SPHS1Ptr is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 370\n", + "Reaction no. 612\n", + "Attempting to remove reaction: SPH1Pter ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4831780000004073\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['HCO3_CLt', 'SBPP1er', 'NDPK5m'], inactive_NC:['SPH1Pter', 'SLCBK1', 'SPHGNtr']\n", + "Reaction SPH1Pter is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 369\n", + "Reaction no. 613\n", + "Attempting to remove reaction: SPHINGStr ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4375169999993886\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['SBPP3er'], inactive_NC:['SPHS1Ptr', 'SPHK21c', 'SPHINGStr']\n", + "Reaction SPHINGStr is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 368\n", + "Reaction no. 614\n", + "Attempting to remove reaction: NMNtn ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2339709999996558\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['NMNATn'], inactive_NC:['NADtn', 'NMNtn']\n", + "Reaction NMNtn is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 367\n", + "Reaction no. 615\n", + "Attempting to remove reaction: DNADtn ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.475388999999268\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['HCO3_CLt', '2HBt2', '2HBO', 'NNATn'], inactive_NC:['DNADtn', 'DNADDP', 'NICRNTtn', 'EX_2hb_e']\n", + "Reaction DNADtn is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 366\n", + "Reaction no. 616\n", + "Attempting to remove reaction: ETOHtx ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3957379999992554\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['CAT2p'], inactive_NC:['ACALDtx', 'ETOHtx']\n", + "Reaction ETOHtx is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 365\n", + "Reaction no. 617\n", + "Attempting to remove reaction: CREATtmdiffir ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1610000000000582\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['CK', 'CKc'], inactive_NC:['PCREATtmdiffir', 'CREATtmdiffir']\n", + "Reaction CREATtmdiffir is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 364\n", + "Reaction no. 618\n", + "Attempting to remove reaction: NICRNTtn ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5102669999996579\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GDHm', 'NNATn'], inactive_NC:['DNADtn', 'DNADDP', 'NICRNTtn']\n", + "Reaction NICRNTtn is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 363\n", + "Reaction no. 619\n", + "Attempting to remove reaction: SPHGNtr ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4423719999995228\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['HCO3_CLt', 'GLUt2m', 'SBPP1er'], inactive_NC:['SPH1Pter', 'SLCBK1', 'SPHGNtr']\n", + "Reaction SPHGNtr is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 362\n", + "Reaction no. 620\n", + "Attempting to remove reaction: ACALDtx ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1971010000006572\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['CAT2p'], inactive_NC:['ACALDtx', 'ETOHtx']\n", + "Reaction ACALDtx is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 361\n", + "Reaction no. 621\n", + "Attempting to remove reaction: DM_datp_n ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1917649999995774\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['GLUt2m', '2HBt2', '2HBO', 'LEUTAm'], inactive_NC:['DATPtn', 'LEUt5m', 'DM_datp_n', 'EX_2hb_e']\n", + "Reaction DM_datp_n is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 360\n", + "Reaction no. 622\n", + "Attempting to remove reaction: DM_dgtp_n ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2948010000000068\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CREATt4_2_r'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'DM_dgtp_n', 'GACMTRc', 'DGTPtn']\n", + "Reaction DM_dgtp_n is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 359\n", + "Reaction no. 623\n", + "Attempting to remove reaction: EX_oxa_e ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4265720000003057\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GCALDD', 'FBA4', 'GLXO1'], inactive_NC:['KHK2', 'EX_oxa_e']\n", + "Reaction EX_oxa_e is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 358\n", + "Reaction no. 624\n", + "Attempting to remove reaction: RTOT_3 ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 35 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4235140000000683\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 36 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'RTOTAL3CRNCPT2', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'RTOTAL3CRNCPT1', 'PGPPT', 'NDPK6n', 'DGAT', 'NDPK5m', 'RTOTAL3CRNt', 'DCYTD', 'RNDR4'], inactive_NC:['THMDt4', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'ARTPLM3m', 'PEFLIP', 'RTOT_3', 'NDP6', 'AHCYStr']\n", + "Reaction RTOT_3 is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 357\n", + "Reaction no. 625\n", + "Attempting to remove reaction: ARTPLM1 ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4117139999998471\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['GLCt1', 'CREATt4_2_r'], inactive_NC:['EX_pi_e', 'EX_creat_e', 'GLYAMDTRc', 'ARTPLM1', 'GACMTRc']\n", + "Reaction ARTPLM1 is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 356\n", + "Reaction no. 626\n", + "Attempting to remove reaction: ARTPLM1m ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4602350000004662\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['RTOTALCRNCPT1', 'CREATt4_2_r', 'RTOTALCRNt', 'PUNP1', 'MTHFD2m', 'RTOTALCRNCPT2'], inactive_NC:['ARTPLM1m', 'GACMTRc', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction ARTPLM1m is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 355\n", + "Reaction no. 627\n", + "Attempting to remove reaction: ARTPLM2m ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.221864000000096\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['RTOTAL2CRNCPT2', 'RTOTAL2CRNCPT1', 'NKCC2t', 'RTOTAL2CRNt'], inactive_NC:['EX_h_e', 'ARTPLM2m']\n", + "Reaction ARTPLM2m is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 354\n", + "Reaction no. 628\n", + "Attempting to remove reaction: ARTPLM3m ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3674929999997403\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['GLCt1', 'RTOTAL3CRNCPT2', 'RTOTAL3CRNCPT1', 'GLUt2m', 'RTOTAL3CRNt'], inactive_NC:['ARTPLM3m']\n", + "Reaction ARTPLM3m is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 353\n", + "Reaction no. 629\n", + "Attempting to remove reaction: HXANtx ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3518590000003314\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['XAO2x'], inactive_NC:['HXANtx']\n", + "Reaction HXANtx is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 352\n", + "Reaction no. 630\n", + "Attempting to remove reaction: H2O2tly ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 257 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.830018999999993\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 258 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'FPGS8', 'FPGS7', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'GGH_7THFl', 'CERT1rt', 'GGH_5THFl', 'SQLSr', 'FPGS4', 'C4STMO2r', 'MTHFCm', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'ACNAM9PL2', 'SOAT12', 'GGH_10FTHF6GLUl', 'GALUi', 'NDPK6n', 'FPGS9m', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'FPGS9', 'G6Pter', 'GLUt2m', 'FPGS5m', 'GGH_10FTHF7GLUl', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'GASNASE2ly', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'FPGS6m', 'LSTO1r', 'GGH_7DHFl', 'DUTPDPn', 'FPGSm', 'AHEXASE2ly', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'FPGS3', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'FPGS3m', 'LSTO2r', 'FPGS7m', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'FPGS2m', 'HEX4', 'A_MANASEly', 'MEVK1x', 'SQLEr', 'SBPP1er', 'NTD3', 'FPGS8m', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'GGH_5DHFl', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'FPGS6', 'GLGNS1', 'UGCG', 'FPGS4m', 'GGH_10FTHF5GLUl', 'PSSA2_hs', 'FPGS', 'DMATTx', 'DHCR242r', 'DHCRD2', 'FPGS5', 'FPGS2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'GGH_6DHFl', 'HSD17B9r', 'DHCR243r', 'GGH_6THFl'], inactive_NC:['H2O2tly', 'ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'THFtm', 'NDP7er', '7DHFtm', 'DHFtm', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', '6DHFtm', 'DHFtl', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', '10FTHFtl', '7THFtm', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'MANtly', 'DM_kdn_c', 'NADPtxu', '7DHFtl', '10FTHF7GLUtm', 'DM_dctp_m', 'EX_estrones_e', '6THFtl', 'DUDPtn', 'GLCt4', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'SARCStex', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'B_MANNASEly', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', '6THFtm', 'XOLTRI25tc', 'XOLTRI25te', 'SARCStm', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'SARDHm', 'KDNH', '10FTHF6GLUtm', '7THFtl', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'ENGASE2ly', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', '10FTHF5GLUtl', 'MEOHtly', 'THFtl', '6DHFtl', 'NADtru', 'HSD3B3r', 'DNDPt52m', '10FTHF5GLUtm', 'DCTPtn', '34HPPOR', 'ATPasel', '10FTHF7GLUtl', 'THMDt4', 'biomass_mac', 'PE_HSter', '5THFtl', 'EX_pe_hs_e', 'DNDPt54m', 'EX_sarcs_e', 'HAS1', 'O2ter', 'DOLPH_Ler', 'EX_n2m2nmasn_e', '5DHFtl', 'NADPtru', 'HAS2', '10FTHF6GLUtl', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'DM_dctp_n', 'AHCYStr', '5THFtm', 'GLUt7l', 'HAtly', 'PRDXl', 'EX_thymd_e', 'SPHK21c', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'N2M2NMASNtly', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'ACGAMtly', 'FALDtly', 'DM_Asn_X_Ser_Thr_l', 'NDP6', 'COAtp']\n", + "Reaction H2O2tly is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 351\n", + "Reaction no. 631\n", + "Attempting to remove reaction: EX_fuc__L_e ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 188 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6591269999998985\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 189 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'FUCASE2e', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'SOAT12', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'GLUt2m', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'MEVK1x', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'EX_xoltri25_e', 'EX_fuc__L_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'NADPtxu', 'EX_ksi_deg1_e', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'GLCt4', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', 'DCTPtn', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'EX_ksi_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'DM_dctp_n', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'NDP6', 'COAtp']\n", + "Reaction EX_fuc__L_e is not in Z\n", + "1492\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 350\n", + "Reaction no. 632\n", + "Attempting to remove reaction: HAtly ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2218209999991814\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['GLCURtly', 'NKCC2t', 'GLCAASE8ly', 'CREATt4_2_r', 'TRIODTHYt2', 'PUNP1', 'GLCAASE9ly', 'NACHEX27ly'], inactive_NC:['EX_creat_e', 'HAtly', 'GLYAMDTRc', 'HAS2', 'HAS1', 'GACMTRc', 'TRIODTHYt']\n", + "Reaction HAtly is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 349\n", + "Reaction no. 633\n", + "Attempting to remove reaction: N2M2NMASNtly ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.472979999999552\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['AHEXASE2ly', 'PUNP1', 'CREATt4_2_r', 'GASNASE2ly'], inactive_NC:['EX_creat_e', 'EX_n2m2nmasn_e', 'GLYAMDTRc', 'N2M2NMASNtly', 'GACMTRc', 'ENGASE2ly']\n", + "Reaction N2M2NMASNtly is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 348\n", + "Reaction no. 634\n", + "Attempting to remove reaction: 7DHFtl ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4278009999998176\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GGH_7DHFl', 'FPGS6m', 'FPGS6'], inactive_NC:['7DHFtl', '7DHFtm']\n", + "Reaction 7DHFtl is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 347\n", + "Reaction no. 635\n", + "Attempting to remove reaction: 7THFtl ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2373349999998027\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['CREATt4_2_r', 'GGH_7THFl', 'FPGS3m', 'FPGS3'], inactive_NC:['7THFtl', 'EX_creat_e', 'GLYAMDTRc', '7THFtm', 'GACMTRc']\n", + "Reaction 7THFtl is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 346\n", + "Reaction no. 636\n", + "Attempting to remove reaction: 10FTHF7GLUtl ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.136279000000286\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['LEUTAm', 'FPGS9', 'SERtN1', 'FPGS9m', 'GGH_10FTHF7GLUl'], inactive_NC:['10FTHF7GLUtm', 'LEUt5m', '10FTHF7GLUtl']\n", + "Reaction 10FTHF7GLUtl is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 345\n", + "Reaction no. 637\n", + "Attempting to remove reaction: VALt5m ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 16 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4420740000005026\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 17 , inactive_C: ['OIVD2m', 'PGM', 'ENO', 'ACOAD9m', 'SERtN1', 'HIBDm', 'HCO3_CLt', 'ECOAH12m', 'VALTAim'], inactive_NC:['MMSAD1m', '3AIBtm', 'MMTSADm', 'EX_3aib_e', 'VALt5m', '3HBCOAHLm', '3AIBTm', '3AIBt']\n", + "Reaction VALt5m is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 344\n", + "Reaction no. 638\n", + "Attempting to remove reaction: ACNML ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 186 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.862699000000248\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 187 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'AMANK', 'GLCAASE9ly', 'FUCASEe', 'SOAT12', 'ACNAM9PL', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'MEVK1x', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'ACNML', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', 'DCTPtn', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'DM_dctp_n', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'ACNAMPH', 'NDP6', 'COAtp']\n", + "Reaction ACNML is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 343\n", + "Reaction no. 639\n", + "Attempting to remove reaction: DITPtn ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1114079999997557\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['GLCt1', 'NDPK10', 'NDPK10n'], inactive_NC:['DIDPtn', 'DITPtn', 'HCO3_NAt']\n", + "Reaction DITPtn is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 342\n", + "Reaction no. 640\n", + "Attempting to remove reaction: DIDPtn ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.152643999999782\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['GLCt1', 'NDPK10', 'NDPK10n', 'HCO3_CLt'], inactive_NC:['DIDPtn', 'DITPtn']\n", + "Reaction DIDPtn is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 341\n", + "Reaction no. 641\n", + "Attempting to remove reaction: ITPtn ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3744460000007166\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['NDPK9n', 'NDPK9'], inactive_NC:['ITPtn', 'NH4t3r', 'IDPtn']\n", + "Reaction ITPtn is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 340\n", + "Reaction no. 642\n", + "Attempting to remove reaction: IDPtn ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.428316999999879\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['NDPK9n', 'NDPK9'], inactive_NC:['ITPtn', 'IDPtn']\n", + "Reaction IDPtn is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 339\n", + "Reaction no. 643\n", + "Attempting to remove reaction: PA_HStn ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1742549999999028\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['DAGKn_hs'], inactive_NC:['PA_HStn', 'MI1P_Dtn', 'PAIL_HStn', 'PIPLCn']\n", + "Reaction PA_HStn is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 338\n", + "Reaction no. 644\n", + "Attempting to remove reaction: DALAxt ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2281419999999343\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['PYRt2p', 'ALAR'], inactive_NC:['DALAxt', 'NH4tp', 'DALAOXx']\n", + "Reaction DALAxt is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 337\n", + "Reaction no. 645\n", + "Attempting to remove reaction: O2Stn ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 29 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4655869999996867\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 30 , inactive_C: ['DUTPDPn', 'NDPK6n', 'SPODMn', 'PI345P3Pn', 'RNDR4', 'DAGKn_hs'], inactive_NC:['PA_HStn', 'PI4P3Kn', 'PI3P3Pn', 'PI34P3Pn', 'DUMPtn', 'PI34P5Kn', 'O2tn', 'PAIL_HStn', 'PI345P5Pn', 'PI45P5Pn', 'PIK4n', 'PI4P4Pn', 'H2O2tn', 'DUDPtn', 'PI3P4Kn', 'PI5P4Kn', 'MI1P_Dtn', 'PI34P4Pn', 'PI45P3Kn', 'PIPLCn', 'PI4P5Kn', 'PIK3n', 'PIK5n', 'O2Stn']\n", + "Reaction O2Stn is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 336\n", + "Reaction no. 646\n", + "Attempting to remove reaction: URATEtx ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 21 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5232420000002094\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 22 , inactive_C: ['PUNP7', 'NTD10', 'DCSPTN1CPT1', 'FAOXC2251836m', 'DCSPTN1CPT2', 'XAO2x', 'XANDp', 'XAOx', 'SERtN1', 'PUNP1', 'DCSPTN1CRNt', 'FAOXC2252053m'], inactive_NC:['URATEtx', 'ADRNCOAtx', 'ARTFR212', 'EX_urate_e', 'HXANtx', 'GUAD', 'DESAT22_1p', 'DCSPTN1COAtx', 'XANtx', 'URATEt']\n", + "Reaction URATEtx is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 335\n", + "Reaction no. 647\n", + "Attempting to remove reaction: FORtr ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 94 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6528629999993427\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 95 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'LEUTAm', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'LEUt5m', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction FORtr is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 334\n", + "Reaction no. 648\n", + "Attempting to remove reaction: EX_nh4_e ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 333\n", + "Reaction no. 649\n", + "Attempting to remove reaction: PE_HSter ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 34 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.243043999999827\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 35 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'LEUTAm', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'DCYTD', 'RNDR4'], inactive_NC:['EX_pi_e', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'GLCt4', 'PCHOLPr_hs', 'PGPP_hs', 'DUMPtn', 'LEUt5m', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'NAHCO3_HCLt', 'NDP6']\n", + "Reaction PE_HSter is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 332\n", + "Reaction no. 650\n", + "Attempting to remove reaction: CO2t ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 331\n", + "Reaction no. 651\n", + "Attempting to remove reaction: S2L2N2M2MASNtly ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 182 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8366820000001098\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 183 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'SOAT12', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'MEVK1x', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', 'DCTPtn', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'DM_dctp_n', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'NDP6', 'COAtp']\n", + "Reaction S2L2N2M2MASNtly is not in Z\n", + "1492\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 330\n", + "Reaction no. 652\n", + "Attempting to remove reaction: OCCOAtm ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4294859999999971\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['NDPK5m', 'PUNP1', 'COAtim'], inactive_NC:['OCCOAtm']\n", + "Reaction OCCOAtm is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 329\n", + "Reaction no. 653\n", + "Attempting to remove reaction: MTHGXLt ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1631029999998646\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['NDPK5m', 'PUNP1'], inactive_NC:['MTHGXLt', 'EX_mthgxl_e']\n", + "Reaction MTHGXLt is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 328\n", + "Reaction no. 654\n", + "Attempting to remove reaction: NH4tp ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1879969999999958\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['GDHm', 'SERtN1', 'ALAR', 'HCO3_CLt', 'PYRt2p'], inactive_NC:['DALAxt', 'NH4tp', 'DALAOXx']\n", + "Reaction NH4tp is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 327\n", + "Reaction no. 655\n", + "Attempting to remove reaction: LRAT1 ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4283809999997175\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['RDH1a', 'PUNP1'], inactive_NC:['RETH2', 'RETI1', 'RETH2e', 'EX_retinol_cis_11_e', 'LRAT1', 'RETFAt2']\n", + "Reaction LRAT1 is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 326\n", + "Reaction no. 656\n", + "Attempting to remove reaction: LRAT2 ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.468735999999808\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['RDH2a', 'PUNP1'], inactive_NC:['RETFAt1', 'EX_retinol_9_cis_e', 'LRAT2', 'RETH1e', 'RETH1', 'RAI2']\n", + "Reaction LRAT2 is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 325\n", + "Reaction no. 657\n", + "Attempting to remove reaction: O2t ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 324\n", + "Reaction no. 658\n", + "Attempting to remove reaction: HMGCOAtx ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 95 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.388546000000133\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 96 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'LEUTAm', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'NDPK5m', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'LEUt5m', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction HMGCOAtx is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 323\n", + "Reaction no. 659\n", + "Attempting to remove reaction: DM_Asn_X_Ser_Thr_l ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 198 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9330700000000434\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 199 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'GDHm', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'ACNAM9PL2', 'SOAT12', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'GASNASE2ly', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'AHEXASE2ly', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'HEX4', 'MEVK1x', 'A_MANASEly', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'MANtly', 'DM_kdn_c', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'B_MANNASEly', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'KDNH', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'ENGASE2ly', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', 'DCTPtn', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'EX_n2m2nmasn_e', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'DM_dctp_n', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'N2M2NMASNtly', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'NH4t3r', 'ACGAMtly', 'DM_Asn_X_Ser_Thr_l', 'NDP6', 'COAtp']\n", + "Reaction DM_Asn_X_Ser_Thr_l is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 934 (119 core, 815 non-core); Num. remaining: 322\n", + "Reaction no. 660\n", + "Attempting to remove reaction: 5THFtl ...\n", + "Initial PM reactions: 1492\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3642190000000483\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['5THFtl']\n", + "Reaction 5THFtl is not in Z\n", + "1492\n", + "1492\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1491\n", + "Num. removed: 935 (119 core, 816 non-core); Num. remaining: 321\n", + "Reaction no. 661\n", + "Attempting to remove reaction: 10FTHF5GLUtl ...\n", + "Initial PM reactions: 1491\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4079959999999119\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CREATt4_2_r', 'GLUt2m'], inactive_NC:['10FTHF5GLUtl', 'GACMTRc', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction 10FTHF5GLUtl is not in Z\n", + "1491\n", + "1491\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 935 (119 core, 816 non-core); Num. remaining: 320\n", + "Reaction no. 662\n", + "Attempting to remove reaction: 6THFtl ...\n", + "Initial PM reactions: 1491\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0995010000006005\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GDHm'], inactive_NC:['6THFtl']\n", + "Reaction 6THFtl is not in Z\n", + "1491\n", + "1491\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 935 (119 core, 816 non-core); Num. remaining: 319\n", + "Reaction no. 663\n", + "Attempting to remove reaction: 10FTHF6GLUtl ...\n", + "Initial PM reactions: 1491\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2734819999996034\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['EX_pi_e', '10FTHF6GLUtl']\n", + "Reaction 10FTHF6GLUtl is not in Z\n", + "1491\n", + "1491\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 935 (119 core, 816 non-core); Num. remaining: 318\n", + "Reaction no. 664\n", + "Attempting to remove reaction: 5DHFtl ...\n", + "Initial PM reactions: 1491\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2169839999996839\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['5DHFtl']\n", + "Reaction 5DHFtl is not in Z\n", + "1491\n", + "1491\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1490\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 317\n", + "Reaction no. 665\n", + "Attempting to remove reaction: 6DHFtl ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1992559999998775\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['SERtN1', 'NKCC2t', 'PUNP5'], inactive_NC:['EX_pi_e', '6DHFtl']\n", + "Reaction 6DHFtl is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 316\n", + "Reaction no. 666\n", + "Attempting to remove reaction: XANtx ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2184240000005957\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['NTD10', 'PUNP1', 'PUNP7'], inactive_NC:['XANtx', 'GUAD']\n", + "Reaction XANtx is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 315\n", + "Reaction no. 667\n", + "Attempting to remove reaction: DHFtm ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3111650000000736\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['FPGS4m', 'FPGS6m', 'FPGS5m'], inactive_NC:['6DHFtm', 'DHFtm', '7DHFtm']\n", + "Reaction DHFtm is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 314\n", + "Reaction no. 668\n", + "Attempting to remove reaction: EX_ala__L_e ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 47 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.501336999999694\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 48 , inactive_C: ['DUTPDPn', 'PROt4', 'PETOHMr_hs', 'SMS', 'PGPPT', 'ALAR', 'DCYTD', 'RNDR4', 'THYMDt1', 'PSSA2_hs', 'HISt4', 'PYRt2p', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'TRPt4', 'NTD3', 'NDPK6n'], inactive_NC:['HCO3_NAt', 'CEPTE', 'PA_HSter', 'EX_ala__L_e', 'EX_his__L_e', 'AHCYStr', 'DALAxt', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'PCHOLPr_hs', 'BTNDe', 'DALAOXx', 'EX_btn_e', 'PGPP_hs', 'EX_biocyt_e', 'DUMPtn', 'VBOF', 'PEFLIP', 'NH4tp', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'EX_pro__L_e', 'NDP6', 'HIStiDF']\n", + "Reaction EX_ala__L_e is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 313\n", + "Reaction no. 669\n", + "Attempting to remove reaction: EX_thr__L_e ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 44 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.212956000000304\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 45 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'PROt4', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'HISt4', 'DCYTD', 'RNDR4', 'TRPt4'], inactive_NC:['EX_pi_e', 'CEPTE', 'PA_HSter', 'EX_his__L_e', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'THRD_L', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'EX_thr__L_e', 'PGPP_hs', 'EX_biocyt_e', 'DUMPtn', 'VBOF', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'EX_pro__L_e', 'NAHCO3_HCLt', 'NDP6', 'HIStiDF']\n", + "Reaction EX_thr__L_e is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 312\n", + "Reaction no. 670\n", + "Attempting to remove reaction: H2O2tn ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 30 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.271509000000151\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 31 , inactive_C: ['DUTPDPn', 'GDHm', 'NDPK6n', 'SPODMn', 'PI345P3Pn', 'RNDR4', 'DAGKn_hs'], inactive_NC:['PA_HStn', 'PI45P5Pn', 'PIK4n', 'PI4P4Pn', 'H2O2tn', 'DUDPtn', 'PI5P4Kn', 'PI34P4Pn', 'PI45P3Kn', 'PIK3n', 'O2Stn', 'PI4P3Kn', 'PI3P3Pn', 'PI34P3Pn', 'DUMPtn', 'PI34P5Kn', 'O2tn', 'PAIL_HStn', 'PI345P5Pn', 'PI3P4Kn', 'MI1P_Dtn', 'PIPLCn', 'PI4P5Kn', 'PIK5n']\n", + "Reaction H2O2tn is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 311\n", + "Reaction no. 671\n", + "Attempting to remove reaction: DM_dctp_m ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4905699999999342\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['NKCC2t', 'TRIODTHYt2'], inactive_NC:['DNDPt53m', 'DNDPt56m', 'DNDPt55m', 'DNDPt51m', 'DNDPt54m', 'DNDPt52m', 'DM_dctp_m', 'TRIODTHYt']\n", + "Reaction DM_dctp_m is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 310\n", + "Reaction no. 672\n", + "Attempting to remove reaction: THFtm ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 19 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4348309999995763\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 20 , inactive_C: ['GDHm', 'FPGS8m', 'FPGSm', 'FPGS7m', 'FPGS3m', 'MTHFCm', 'FPGS9m', 'NDPK5m', 'FPGS2m'], inactive_NC:['5THFtm', 'SARCStm', 'SARCStex', 'SARDHm', '6THFtm', '7THFtm', 'THFtm', '10FTHF5GLUtm', 'EX_sarcs_e', '10FTHF7GLUtm', '10FTHF6GLUtm']\n", + "Reaction THFtm is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 309\n", + "Reaction no. 673\n", + "Attempting to remove reaction: ASNtm ...\n", + "Initial PM reactions: 1490\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1584439999996903\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['ASNNm', 'ASNtm', 'GLYtm']\n", + "Reaction ASNtm is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 308\n", + "Reaction no. 674\n", + "Attempting to remove reaction: MI1P_Dtn ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1828980000000229\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['DAGKn_hs'], inactive_NC:['PA_HStn', 'MI1P_Dtn', 'PAIL_HStn', 'PIPLCn']\n", + "Reaction MI1P_Dtn is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 307\n", + "Reaction no. 675\n", + "Attempting to remove reaction: DM_datp_m ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4058589999995093\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['NDPK5m'], inactive_NC:['DM_datp_m']\n", + "Reaction DM_datp_m is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 306\n", + "Reaction no. 676\n", + "Attempting to remove reaction: EX_met__L_e ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 47 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6656669999993028\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 48 , inactive_C: ['DUTPDPn', 'PROt4', 'PETOHMr_hs', 'SMS', 'PGPPT', 'DCYTD', 'RNDR4', 'THYMDt1', 'PSSA2_hs', 'HISt4', 'CYSTS', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'NDPK5m', 'METLEUex', 'TRPt4', 'NTD3', 'NDPK6n', 'METt4'], inactive_NC:['CYSTGL', 'CEPTE', 'PA_HSter', 'EX_his__L_e', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'PGPP_hs', 'EX_biocyt_e', 'DUMPtn', 'VBOF', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'NH4t3r', 'EX_pro__L_e', 'EX_met__L_e', 'NDP6', 'HIStiDF']\n", + "Reaction EX_met__L_e is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 305\n", + "Reaction no. 677\n", + "Attempting to remove reaction: RAtn3 ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.176514999999199\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['CREATt4_2_r', 'RAI3'], inactive_NC:['DM_13_cis_retn_n', 'EX_creat_e', 'GLYAMDTRc', 'RAtn3', 'RETNt', 'EX_retn_e', 'GACMTRc']\n", + "Reaction RAtn3 is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 304\n", + "Reaction no. 678\n", + "Attempting to remove reaction: RETNt ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1982410000000527\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['RAI3', 'GDHm'], inactive_NC:['RAtn3', 'DM_13_cis_retn_n', 'EX_retn_e', 'RETNt']\n", + "Reaction RETNt is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 303\n", + "Reaction no. 679\n", + "Attempting to remove reaction: PI4P4Pn ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 12 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.371487000000343\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 13 , inactive_C: ['NKCC2t', 'CREATt4_2_r', 'TRIODTHYt2', 'LEUTAm', 'MECOAS1m', 'NDPK5m', 'MECOALm'], inactive_NC:['EX_creat_e', 'PI4P4Pn', 'GLYAMDTRc', 'LEUt5m', 'GACMTRc', 'TRIODTHYt']\n", + "Reaction PI4P4Pn is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 302\n", + "Reaction no. 680\n", + "Attempting to remove reaction: PI345P5Pn ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4683210000002873\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['2HBt2', 'PUNP1', 'NKCC2t', '2HBO'], inactive_NC:['PI345P5Pn', 'EX_2hb_e']\n", + "Reaction PI345P5Pn is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 301\n", + "Reaction no. 681\n", + "Attempting to remove reaction: PI34P3Pn ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.146694000000025\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CREATt4_2_r', 'PUNP1'], inactive_NC:['GACMTRc', 'EX_creat_e', 'PI34P3Pn', 'GLYAMDTRc']\n", + "Reaction PI34P3Pn is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 300\n", + "Reaction no. 682\n", + "Attempting to remove reaction: PI34P4Pn ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2943560000003345\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CREATt4_2_r', 'GLUt2m'], inactive_NC:['PI34P4Pn', 'GACMTRc', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction PI34P4Pn is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 299\n", + "Reaction no. 683\n", + "Attempting to remove reaction: PI3P3Pn ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.399373000000196\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['TRIODTHYt2', 'NKCC2t', 'PUNP1', 'GDHm'], inactive_NC:['PI3P3Pn', 'TRIODTHYt']\n", + "Reaction PI3P3Pn is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 298\n", + "Reaction no. 684\n", + "Attempting to remove reaction: PI45P5Pn ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4019869999992807\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GDHm'], inactive_NC:['PI45P5Pn']\n", + "Reaction PI45P5Pn is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 297\n", + "Reaction no. 685\n", + "Attempting to remove reaction: DUMPtn ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2079420000000027\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['NDPK6n', 'NKCC2t', 'DUTPDPn', 'RNDR4'], inactive_NC:['DUDPtn', 'DUMPtn']\n", + "Reaction DUMPtn is not in Z\n", + "1490\n", + "1490\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 936 (119 core, 817 non-core); Num. remaining: 296\n", + "Reaction no. 686\n", + "Attempting to remove reaction: DM_dgtp_m ...\n", + "Initial PM reactions: 1490\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3685059999997975\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['DM_dgtp_m']\n", + "Reaction DM_dgtp_m is not in Z\n", + "1490\n", + "1490\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1489\n", + "Num. removed: 937 (119 core, 818 non-core); Num. remaining: 295\n", + "Reaction no. 687\n", + "Attempting to remove reaction: DCTPtn ...\n", + "Initial PM reactions: 1489\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4180560000004334\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['DCTPtn', 'DM_dctp_n']\n", + "Reaction DCTPtn is not in Z\n", + "1489\n", + "1489\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1487\n", + "Num. removed: 939 (119 core, 820 non-core); Num. remaining: 294\n", + "Reaction no. 688\n", + "Attempting to remove reaction: GLCMter ...\n", + "Initial PM reactions: 1487\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 52 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4441829999996116\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 53 , inactive_C: ['UDPDOLPT_U', 'DUTPDPn', 'PETOHMr_hs', 'SMS', 'PGPPT', 'DCYTD', 'UDPDOLPT_L', 'NDPK7', 'RNDR4', 'THYMDt1', 'RNDR3', 'PSSA2_hs', 'G6Pter', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'NTD3', 'NDPK6n'], inactive_NC:['DOLPH_Ler', 'DNDPt56m', 'CEPTE', 'DOLGPP_Uer', 'PA_HSter', 'DOLGLCP_Uter', 'DOLP_Uter', 'DM_dctp_m', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'DNDPt55m', 'DOLICHOL_Lter', 'PCHOLPr_hs', 'PGPP_hs', 'DOLGPP_Ler', 'GLCMter', 'DOLP_Lter', 'DUMPtn', 'G6PPer', 'DOLGLCP_Lter', 'DNDPt52m', 'PEFLIP', 'THMDt4', 'biomass_mac', 'DNDPt53m', 'PE_HSter', 'DOLK_L', 'EX_pe_hs_e', 'DNDPt51m', 'DNDPt54m', 'NDP6']\n", + "Reaction GLCMter is not in Z\n", + "1487\n", + "1487\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 939 (119 core, 820 non-core); Num. remaining: 293\n", + "Reaction no. 689\n", + "Attempting to remove reaction: GLNtm ...\n", + "Initial PM reactions: 1487\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1817849999997634\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['GLUNm', 'GDHm'], inactive_NC:['GLNtm']\n", + "Reaction GLNtm is not in Z\n", + "1487\n", + "1487\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 939 (119 core, 820 non-core); Num. remaining: 292\n", + "Reaction no. 690\n", + "Attempting to remove reaction: DHFtl ...\n", + "Initial PM reactions: 1487\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4673290000000634\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['GGH_7DHFl', 'FPGS4m', 'GGH_5DHFl', 'FPGS5', 'FPGS4', 'GGH_6DHFl', 'FPGS6m', 'FPGS5m', 'FPGS6'], inactive_NC:['6DHFtm', 'DHFtl', '6DHFtl', '7DHFtl', '7DHFtm', 'DHFtm']\n", + "Reaction DHFtl is not in Z\n", + "1487\n", + "1487\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 939 (119 core, 820 non-core); Num. remaining: 291\n", + "Reaction no. 691\n", + "Attempting to remove reaction: 10FTHFtl ...\n", + "Initial PM reactions: 1487\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 23 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2587540000004083\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 24 , inactive_C: ['GGH_10FTHF5GLUl', 'NKCC2t', 'FPGS8m', 'TRIODTHYt2', 'FPGS7m', 'GGH_10FTHF6GLUl', 'FPGS9', 'MTHFCm', 'FPGS9m', 'FPGS8', 'FPGS7', 'GGH_10FTHF7GLUl'], inactive_NC:['SARCStm', '10FTHF5GLUtl', '10FTHF6GLUtl', '10FTHFtl', 'SARCStex', 'SARDHm', '10FTHF5GLUtm', 'EX_sarcs_e', '10FTHF7GLUtm', '10FTHF6GLUtm', 'TRIODTHYt', '10FTHF7GLUtl']\n", + "Reaction 10FTHFtl is not in Z\n", + "1487\n", + "1487\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 939 (119 core, 820 non-core); Num. remaining: 290\n", + "Reaction no. 692\n", + "Attempting to remove reaction: NADHtpu ...\n", + "Initial PM reactions: 1487\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2050579999995534\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['NKCC2t', 'GDHm'], inactive_NC:['NADHtpu', 'NADtpu']\n", + "Reaction NADHtpu is not in Z\n", + "1487\n", + "1487\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 939 (119 core, 820 non-core); Num. remaining: 289\n", + "Reaction no. 693\n", + "Attempting to remove reaction: NADtpu ...\n", + "Initial PM reactions: 1487\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1314940000002025\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['NKCC2t', 'TRIODTHYt2'], inactive_NC:['NADHtpu', 'NADtpu', 'TRIODTHYt']\n", + "Reaction NADtpu is not in Z\n", + "1487\n", + "1487\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 939 (119 core, 820 non-core); Num. remaining: 288\n", + "Reaction no. 694\n", + "Attempting to remove reaction: THFtl ...\n", + "Initial PM reactions: 1487\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 15 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5252080000000205\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 16 , inactive_C: ['GGH_7THFl', 'GGH_5THFl', 'FPGS2', 'FPGSm', 'FPGS3m', 'FPGS', 'GGH_6THFl', 'FPGS2m', 'FPGS3'], inactive_NC:['5THFtm', '7THFtl', 'EX_pi_e', 'THFtl', '6THFtm', '7THFtm', '6THFtl']\n", + "Reaction THFtl is not in Z\n", + "1487\n", + "1487\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 939 (119 core, 820 non-core); Num. remaining: 287\n", + "Reaction no. 695\n", + "Attempting to remove reaction: CHOLtr ...\n", + "Initial PM reactions: 1487\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 30 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.647382000000107\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 31 , inactive_C: ['THYMDt1', 'DUTPDPn', 'GDHm', 'PSSA2_hs', 'FACOAL161', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'DCYTD', 'RNDR4'], inactive_NC:['THMDt4', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'PEFLIP', 'NDP6', 'AHCYStr']\n", + "Reaction CHOLtr is not in Z\n", + "1487\n", + "1487\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 939 (119 core, 820 non-core); Num. remaining: 286\n", + "Reaction no. 696\n", + "Attempting to remove reaction: O2tn ...\n", + "Initial PM reactions: 1487\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 33 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1828969999996843\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 34 , inactive_C: ['NKCC2t', 'DUTPDPn', 'TRIODTHYt2', 'NDPK6n', 'SERtN1', 'SPODMn', 'PI345P3Pn', 'RNDR4', 'DAGKn_hs'], inactive_NC:['PA_HStn', 'TRIODTHYt', 'PI45P5Pn', 'PIK4n', 'PI4P4Pn', 'H2O2tn', 'DUDPtn', 'PI5P4Kn', 'PI34P4Pn', 'PI45P3Kn', 'PIK3n', 'O2Stn', 'PI4P3Kn', 'PI3P3Pn', 'PI34P3Pn', 'DUMPtn', 'PI34P5Kn', 'O2tn', 'PAIL_HStn', 'PI345P5Pn', 'PI3P4Kn', 'MI1P_Dtn', 'PIPLCn', 'PI4P5Kn', 'PIK5n']\n", + "Reaction O2tn is not in Z\n", + "1487\n", + "1487\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 939 (119 core, 820 non-core); Num. remaining: 285\n", + "Reaction no. 697\n", + "Attempting to remove reaction: DATPtn ...\n", + "Initial PM reactions: 1487\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3579129999998258\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: [], inactive_NC:['NAHCO3_HCLt', 'DATPtn', 'DM_datp_n']\n", + "Reaction DATPtn is not in Z\n", + "1487\n", + "1487\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1484\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 283\n", + "Reaction no. 698\n", + "Attempting to remove reaction: NADtn ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4487069999995583\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['NMNATn', 'TRIODTHYt2'], inactive_NC:['EX_pi_e', 'EX_nh4_e', 'NH4t3r', 'NMNtn', 'NADtn', 'TRIODTHYt']\n", + "Reaction NADtn is not in Z\n", + "1484\n", + "1484\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 282\n", + "Reaction no. 699\n", + "Attempting to remove reaction: DGTPtn ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2804360000000088\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['FTHFLi', 'MTHFC', 'MTHFD'], inactive_NC:['DGTPtn', 'DM_dgtp_n']\n", + "Reaction DGTPtn is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 281\n", + "Reaction no. 700\n", + "Attempting to remove reaction: O2tm ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 280\n", + "Reaction no. 701\n", + "Attempting to remove reaction: CHSTEROLt2 ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 36 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5672919999997248\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 37 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'SOAT12', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'SERtN1', 'DGAT', 'DCYTD', 'RNDR4', 'SOAT11'], inactive_NC:['CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'PCHOLPr_hs', 'PGPP_hs', 'DUMPtn', 'CHSTEROLt3', 'PEFLIP', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'NDP6']\n", + "Reaction CHSTEROLt2 is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 279\n", + "Reaction no. 702\n", + "Attempting to remove reaction: ESTRONEtr ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4526080000005095\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['HCO3_CLt', 'HSD17B7r', 'HSD17B8r'], inactive_NC:['P4501B1r', 'HESTRATRIOLtr', 'EX_hestratriol_e', 'ESTRONESt2', 'ESTRONEtr', 'HESTRATRIOLte', 'EX_estrones_e']\n", + "Reaction ESTRONEtr is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 278\n", + "Reaction no. 703\n", + "Attempting to remove reaction: CO2ter ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 93 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4442470000003595\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 94 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'GLCt4', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction CO2ter is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 277\n", + "Reaction no. 704\n", + "Attempting to remove reaction: NADPHtxu ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 92 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6611839999995937\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 93 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction NADPHtxu is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 276\n", + "Reaction no. 705\n", + "Attempting to remove reaction: NADPtxu ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 93 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6268159999999625\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 94 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'GLCt4', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction NADPtxu is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 275\n", + "Reaction no. 706\n", + "Attempting to remove reaction: EX_pi_e ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 274\n", + "Reaction no. 707\n", + "Attempting to remove reaction: EX_h_e ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 273\n", + "Reaction no. 708\n", + "Attempting to remove reaction: CO2tp ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 94 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3716160000003583\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 95 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['EX_pi_e', 'PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'GLCt4', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction CO2tp is not in Z\n", + "1484\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 272\n", + "Reaction no. 709\n", + "Attempting to remove reaction: NADHtru ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3258259999993243\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['TRIODTHYt2', 'SERtN1', 'NKCC2t', 'GDHm'], inactive_NC:['NADtru', 'EX_pi_e', 'TRIODTHYt', 'NADHtru']\n", + "Reaction NADHtru is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 271\n", + "Reaction no. 710\n", + "Attempting to remove reaction: NADtru ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2820730000003095\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['PUNP1'], inactive_NC:['NADtru', 'EX_pi_e', 'NADHtru']\n", + "Reaction NADtru is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 270\n", + "Reaction no. 711\n", + "Attempting to remove reaction: EX_ins_e ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1665960000000268\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['HCO3_CLt'], inactive_NC:['EX_ins_e']\n", + "Reaction EX_ins_e is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 269\n", + "Reaction no. 712\n", + "Attempting to remove reaction: 2AMACSULT ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.440107999999782\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['CREATt4_2_r', 'NKCC2t', 'PUNP1'], inactive_NC:['GACMTRc', 'EX_creat_e', '2AMACSULT', 'GLYAMDTRc']\n", + "Reaction 2AMACSULT is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 268\n", + "Reaction no. 713\n", + "Attempting to remove reaction: FRDPtr ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 94 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.670114000000467\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 95 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['EX_pi_e', 'PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'GLCt4', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction FRDPtr is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 267\n", + "Reaction no. 714\n", + "Attempting to remove reaction: EX_thymd_e ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2850960000005216\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['THYMDt1'], inactive_NC:['THMDt4', 'EX_thymd_e']\n", + "Reaction EX_thymd_e is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 266\n", + "Reaction no. 715\n", + "Attempting to remove reaction: EX_orn_e ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.141605000000709\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['ORNt'], inactive_NC:['EX_orn_e']\n", + "Reaction EX_orn_e is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 265\n", + "Reaction no. 716\n", + "Attempting to remove reaction: ACGAMtly ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 194 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7291580000000977\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 195 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'ACNAM9PL2', 'SOAT12', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'GASNASE2ly', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'AHEXASE2ly', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'HEX4', 'MEVK1x', 'A_MANASEly', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'MANtly', 'DM_kdn_c', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'B_MANNASEly', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'KDNH', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'ENGASE2ly', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'EX_n2m2nmasn_e', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'N2M2NMASNtly', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'ACGAMtly', 'DM_Asn_X_Ser_Thr_l', 'NDP6', 'COAtp']\n", + "Reaction ACGAMtly is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 264\n", + "Reaction no. 717\n", + "Attempting to remove reaction: GALtly ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 181 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 2.038144000000102\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 182 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'GDHm', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'SOAT12', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'MEVK1x', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'NDP6', 'COAtp']\n", + "Reaction GALtly is not in Z\n", + "1484\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 263\n", + "Reaction no. 718\n", + "Attempting to remove reaction: EX_arg__L_e ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4053659999999581\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['ARGt4', 'LEUTAm', 'PUNP1', 'ARGLYSex', 'ARGt5r'], inactive_NC:['LEUt5m', 'EX_arg__L_e']\n", + "Reaction EX_arg__L_e is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 262\n", + "Reaction no. 719\n", + "Attempting to remove reaction: UDPGLCter ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2065919999995458\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['CERT1rt', 'UGCG', 'CERT2rt', 'GBA'], inactive_NC:['UDPGLCter', 'NDP7er', 'HCO3_NAt']\n", + "Reaction UDPGLCter is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 261\n", + "Reaction no. 720\n", + "Attempting to remove reaction: ARTFR45 ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1367510000000038\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['PUNP1', 'FACOAL241'], inactive_NC:['EX_nrvnc_e', 'FATP9t', 'ARTFR45']\n", + "Reaction ARTFR45 is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 260\n", + "Reaction no. 721\n", + "Attempting to remove reaction: EX_5mthf_e ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.395169000000351\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['5MTHFt', 'TRIODTHYt2', 'FOLR2'], inactive_NC:['EX_5mthf_e', 'FOLt2', 'EX_fol_e', 'TRIODTHYt']\n", + "Reaction EX_5mthf_e is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 259\n", + "Reaction no. 722\n", + "Attempting to remove reaction: ARTFR43 ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4292310000000725\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['HCO3_CLt', 'PUNP1'], inactive_NC:['ARTFR43']\n", + "Reaction ARTFR43 is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 258\n", + "Reaction no. 723\n", + "Attempting to remove reaction: ARTFR41 ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2168280000005325\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['PUNP1'], inactive_NC:['ARTFR41']\n", + "Reaction ARTFR41 is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 257\n", + "Reaction no. 724\n", + "Attempting to remove reaction: ARTFR42 ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1688340000000608\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PUNP1'], inactive_NC:['ARTFR42', 'HCO3_NAt']\n", + "Reaction ARTFR42 is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 256\n", + "Reaction no. 725\n", + "Attempting to remove reaction: ARTFR46 ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.359745999999177\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['LEUTAm'], inactive_NC:['LEUt5m', 'ARTFR46', 'HCO3_NAt']\n", + "Reaction ARTFR46 is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 942 (119 core, 823 non-core); Num. remaining: 255\n", + "Reaction no. 726\n", + "Attempting to remove reaction: ARTFR44 ...\n", + "Initial PM reactions: 1484\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.238322000000153\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['ARTFR44']\n", + "Reaction ARTFR44 is not in Z\n", + "1484\n", + "1484\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1483\n", + "Num. removed: 943 (119 core, 824 non-core); Num. remaining: 254\n", + "Reaction no. 727\n", + "Attempting to remove reaction: CYSGLTH ...\n", + "Initial PM reactions: 1483\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1657930000001215\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['HCO3_CLt', 'CYSTGLUex'], inactive_NC:['CYSTSERex', 'EX_cysi__L_e', 'CYSGLTH']\n", + "Reaction CYSGLTH is not in Z\n", + "1483\n", + "1483\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 943 (119 core, 824 non-core); Num. remaining: 253\n", + "Reaction no. 728\n", + "Attempting to remove reaction: ARTFR12 ...\n", + "Initial PM reactions: 1483\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1439180000006672\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['NKCC2t'], inactive_NC:['ARTFR12', 'EX_pi_e']\n", + "Reaction ARTFR12 is not in Z\n", + "1483\n", + "1483\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 943 (119 core, 824 non-core); Num. remaining: 252\n", + "Reaction no. 729\n", + "Attempting to remove reaction: DOLPH_Ler ...\n", + "Initial PM reactions: 1483\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 48 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5833149999998568\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 49 , inactive_C: ['DUTPDPn', 'PETOHMr_hs', 'SMS', 'PGPPT', 'DCYTD', 'NDPK7', 'RNDR4', 'THYMDt1', 'RNDR3', 'PSSA2_hs', 'CREATt4_2_r', 'TRIODTHYt2', 'SERtN1', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'NTD3', 'NDPK6n'], inactive_NC:['DOLPH_Ler', 'DNDPt56m', 'CEPTE', 'PA_HSter', 'GACMTRc', 'DM_dctp_m', 'TRIODTHYt', 'AHCYStr', 'EX_creat_e', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'DNDPt55m', 'DOLICHOL_Lter', 'PCHOLPr_hs', 'PGPP_hs', 'DUMPtn', 'DNDPt52m', 'PEFLIP', 'THMDt4', 'GLYAMDTRc', 'biomass_mac', 'DNDPt53m', 'PE_HSter', 'DOLK_L', 'EX_pe_hs_e', 'DNDPt51m', 'DNDPt54m', 'NDP6']\n", + "Reaction DOLPH_Ler is not in Z\n", + "1483\n", + "1483\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 943 (119 core, 824 non-core); Num. remaining: 251\n", + "Reaction no. 730\n", + "Attempting to remove reaction: DUDPtn ...\n", + "Initial PM reactions: 1483\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4133460000002742\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['DUTPDPn', 'CREATt4_2_r', 'NDPK6n', 'PUNP1', 'RNDR4'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'DUDPtn', 'DUMPtn', 'GACMTRc']\n", + "Reaction DUDPtn is not in Z\n", + "1483\n", + "1483\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 943 (119 core, 824 non-core); Num. remaining: 250\n", + "Reaction no. 731\n", + "Attempting to remove reaction: GTHDH ...\n", + "Initial PM reactions: 1483\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1379680000000008\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['GTHDH']\n", + "Reaction GTHDH is not in Z\n", + "1483\n", + "1483\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1482\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 249\n", + "Reaction no. 732\n", + "Attempting to remove reaction: DESAT22_1p ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 12 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4709619999994175\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 13 , inactive_C: ['NKCC2t', 'DCSPTN1CPT1', 'FAOXC2251836m', 'DCSPTN1CPT2', 'TRIODTHYt2', 'XANDp', 'DCSPTN1CRNt', 'FAOXC2252053m'], inactive_NC:['ADRNCOAtx', 'ARTFR212', 'DESAT22_1p', 'DCSPTN1COAtx', 'TRIODTHYt']\n", + "Reaction DESAT22_1p is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 248\n", + "Reaction no. 733\n", + "Attempting to remove reaction: O2ter ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 149 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9446969999999055\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 150 , inactive_C: ['UDPDOLPT_U', 'DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'HSD17B8r', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'GBA', 'PUNP1', 'EBP1r', 'HMGCOARx', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'UGCG', 'THYMDt1', 'RNDR3', 'PSSA2_hs', 'C4STMO2Pr', 'G6Pter', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'CERT1rt', 'SQLSr', 'DHCRD2', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'SBPP3er', 'DGAT', 'DHCR72r', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'SBPP1er', 'HSD17B9r', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'HSD17B7r', 'NDPK6n', 'CERT2rt', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'HSD3A1r', 'NADHtru', 'HMGCOAtx', 'SPH1Pter', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'DOLP_Lter', 'PROD2', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', '34HPPOR', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'O2ter', 'DOLPH_Ler', 'NADPtru', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'AHCYStr', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'NDP6', 'COAtp']\n", + "Reaction O2ter is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 247\n", + "Reaction no. 734\n", + "Attempting to remove reaction: EX_urea_e ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2104449999997087\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['ARGSL', 'ARGSS', 'PUNP1', 'CBPSam', 'ARGNm', 'UREAt'], inactive_NC:['OCBTm', 'CITRtm', 'UREAtm', 'ARGtm', 'EX_urea_e']\n", + "Reaction EX_urea_e is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 246\n", + "Reaction no. 735\n", + "Attempting to remove reaction: PPAn ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.161949000000277\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['DUTPDPn', 'NMNATn', 'GLUt2m', 'NDPK6n', 'NNATn', 'RNDR4'], inactive_NC:['DNADDP', 'DUDPtn', 'DUMPtn', 'NICRNTtn', 'ATPtn', 'PPAn', 'NMNtn', 'DNADtn', 'NADtn']\n", + "Reaction PPAn is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 245\n", + "Reaction no. 736\n", + "Attempting to remove reaction: PItn ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 30 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4529529999999795\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 31 , inactive_C: ['DUTPDPn', 'NMNATn', 'NDPK6n', 'PI345P3Pn', 'NNATn', 'RNDR4'], inactive_NC:['PI4P3Kn', 'PI3P3Pn', 'PI34P3Pn', 'DUMPtn', 'NICRNTtn', 'PI34P5Kn', 'PPAn', 'NMNtn', 'NADtn', 'PI345P5Pn', 'PI45P5Pn', 'PI4P5Kn', 'PIK4n', 'DNADDP', 'PI4P4Pn', 'PItn', 'DUDPtn', 'PI3P4Kn', 'PI5P4Kn', 'ATPtn', 'PI34P4Pn', 'PI45P3Kn', 'DNADtn', 'PIK3n', 'PIK5n']\n", + "Reaction PItn is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 244\n", + "Reaction no. 737\n", + "Attempting to remove reaction: EX_leu__L_e ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 47 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5091029999994134\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 48 , inactive_C: ['DUTPDPn', 'PROt4', 'PETOHMr_hs', 'SMS', 'PGPPT', 'DCYTD', 'RNDR4', 'THYMDt1', 'PSSA2_hs', 'HMGLm', 'SERtN1', 'HISt4', 'OIVD1m', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'TRPt4', 'NTD3', 'MGCHrm', 'NDPK6n'], inactive_NC:['CEPTE', 'PA_HSter', 'EX_his__L_e', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_leu__L_e', 'EX_trp__L_e', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'MCCCrm', 'PGPP_hs', 'EX_biocyt_e', 'ACOAD8m', 'DUMPtn', 'VBOF', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'EX_pro__L_e', 'NDP6', 'HIStiDF']\n", + "Reaction EX_leu__L_e is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 243\n", + "Reaction no. 738\n", + "Attempting to remove reaction: MANtly ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 197 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6116919999994934\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 198 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'GDHm', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'ACNAM9PL2', 'SOAT12', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'SERtN1', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'GASNASE2ly', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'AHEXASE2ly', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'HEX4', 'MEVK1x', 'A_MANASEly', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'MANtly', 'DM_kdn_c', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'GLCt4', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'B_MANNASEly', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'KDNH', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'ENGASE2ly', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'EX_n2m2nmasn_e', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'N2M2NMASNtly', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'ACGAMtly', 'DM_Asn_X_Ser_Thr_l', 'NDP6', 'COAtp']\n", + "Reaction MANtly is not in Z\n", + "1482\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 242\n", + "Reaction no. 739\n", + "Attempting to remove reaction: PItx ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 92 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7109539999992194\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 93 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction PItx is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 241\n", + "Reaction no. 740\n", + "Attempting to remove reaction: MDRPD ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 12 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.460320999999567\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 13 , inactive_C: ['SPMS', 'MTAP', 'SPRMS', 'BAMPPALDOX', 'ADMDC'], inactive_NC:['DM_sprm_c', '13DAMPPOX', 'UNK2', 'UNK3', 'SPMDOX', 'MDRPD', 'MTRI', 'DKMPPD']\n", + "Reaction MDRPD is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 240\n", + "Reaction no. 741\n", + "Attempting to remove reaction: LEUt5m ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 239\n", + "Reaction no. 742\n", + "Attempting to remove reaction: DRPA ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 12 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2436619999998584\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 13 , inactive_C: ['GDHm', 'DADAe', 'CREATt4_2_r', 'DADA', 'PUNP6'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'DINt', 'DRPA', 'DRBK', 'GLCt4', '2DR1PP', 'GACMTRc']\n", + "Reaction DRPA is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 238\n", + "Reaction no. 743\n", + "Attempting to remove reaction: UNK3 ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1291570000003048\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['NKCC2t', 'TRIODTHYt2'], inactive_NC:['UNK3', 'TRIODTHYt']\n", + "Reaction UNK3 is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 237\n", + "Reaction no. 744\n", + "Attempting to remove reaction: EX_ile__L_e ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 49 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6233249999995678\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 50 , inactive_C: ['ACOAD10m', 'DUTPDPn', 'PROt4', 'PETOHMr_hs', 'SMS', 'PGPPT', 'DCYTD', 'RNDR4', 'ILEt4', 'THYMDt1', 'PSSA2_hs', 'HISt4', 'HACD9m', 'OIVD3m', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', 'ECOAH9m', 'TRPt4', 'NTD3', 'NDPK6n'], inactive_NC:['CEPTE', 'PA_HSter', 'EX_ile__L_e', 'EX_his__L_e', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'PGPP_hs', 'EX_biocyt_e', 'ILETA', 'DUMPtn', 'VBOF', 'PEFLIP', 'THMDt4', 'biomass_mac', 'ACACT10m', 'PE_HSter', 'EX_pe_hs_e', '3MOPt2im', 'EX_pro__L_e', 'NDP6', 'HIStiDF']\n", + "Reaction EX_ile__L_e is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 236\n", + "Reaction no. 745\n", + "Attempting to remove reaction: SPMDOX ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3891340000000127\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['BAMPPALDOX', 'NKCC2t', 'GDHm'], inactive_NC:['13DAMPPOX', 'EX_pi_e', 'SPMDOX']\n", + "Reaction SPMDOX is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 235\n", + "Reaction no. 746\n", + "Attempting to remove reaction: TMDPPK ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 12 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1554059999998572\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 13 , inactive_C: ['THMTP', '5MTHFt', 'THMt3', 'PUNP1', 'FOLR2'], inactive_NC:['EX_thm_e', 'TMDPPK', 'FOLt2', 'EX_thmtp_e', 'CLOHtex2', 'EX_5mthf_e', 'EX_fol_e', 'THMTPt']\n", + "Reaction TMDPPK is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 944 (119 core, 825 non-core); Num. remaining: 234\n", + "Reaction no. 747\n", + "Attempting to remove reaction: 2AMACHYD ...\n", + "Initial PM reactions: 1482\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.112981999999647\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['2AMACHYD']\n", + "Reaction 2AMACHYD is not in Z\n", + "1482\n", + "1482\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1481\n", + "Num. removed: 945 (119 core, 826 non-core); Num. remaining: 233\n", + "Reaction no. 748\n", + "Attempting to remove reaction: NADPHtru ...\n", + "Initial PM reactions: 1481\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 148 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4739419999996244\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 149 , inactive_C: ['UDPDOLPT_U', 'DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'HSD17B8r', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'GBA', 'EBP1r', 'HMGCOARx', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'UGCG', 'THYMDt1', 'RNDR3', 'PSSA2_hs', 'C4STMO2Pr', 'G6Pter', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'CERT1rt', 'SQLSr', 'DHCRD2', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'SBPP3er', 'DGAT', 'DHCR72r', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'SBPP1er', 'HSD17B9r', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'HSD17B7r', 'NDPK6n', 'CERT2rt', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'HSD3A1r', 'NADHtru', 'HMGCOAtx', 'SPH1Pter', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'DOLP_Lter', 'PROD2', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', '34HPPOR', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'O2ter', 'DOLPH_Ler', 'NADPtru', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'AHCYStr', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'NDP6', 'COAtp']\n", + "Reaction NADPHtru is not in Z\n", + "1481\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1481\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 945 (119 core, 826 non-core); Num. remaining: 232\n", + "Reaction no. 749\n", + "Attempting to remove reaction: NADPtru ...\n", + "Initial PM reactions: 1481\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 149 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6020779999998922\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 150 , inactive_C: ['UDPDOLPT_U', 'DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'HSD17B8r', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'GBA', 'PUNP1', 'EBP1r', 'HMGCOARx', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'UGCG', 'THYMDt1', 'RNDR3', 'PSSA2_hs', 'C4STMO2Pr', 'G6Pter', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'CERT1rt', 'SQLSr', 'DHCRD2', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'SBPP3er', 'DGAT', 'DHCR72r', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'SBPP1er', 'HSD17B9r', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'HSD17B7r', 'NDPK6n', 'CERT2rt', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'HSD3A1r', 'NADHtru', 'HMGCOAtx', 'SPH1Pter', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'DOLP_Lter', 'PROD2', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', '34HPPOR', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'O2ter', 'DOLPH_Ler', 'NADPtru', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'AHCYStr', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'NDP6', 'COAtp']\n", + "Reaction NADPtru is not in Z\n", + "1481\n", + "1481\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 945 (119 core, 826 non-core); Num. remaining: 231\n", + "Reaction no. 750\n", + "Attempting to remove reaction: DGK2m ...\n", + "Initial PM reactions: 1481\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4367490000004182\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['PUNP1', 'NTD8', 'DGNSKm'], inactive_NC:['DGK2m', 'DGSNtm']\n", + "Reaction DGK2m is not in Z\n", + "1481\n", + "1481\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 945 (119 core, 826 non-core); Num. remaining: 230\n", + "Reaction no. 751\n", + "Attempting to remove reaction: H2Otn ...\n", + "Initial PM reactions: 1481\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 42 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5016900000000533\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 43 , inactive_C: ['DUTPDPn', 'NMNATn', 'NDPK6n', 'SERtN1', 'SPODMn', 'PI345P3Pn', 'NNATn', 'HCO3_CLt', 'RNDR4', 'DAGKn_hs'], inactive_NC:['PA_HStn', 'PPAn', 'NMNtn', 'NADtn', 'PI45P5Pn', 'PIK4n', 'PI4P4Pn', 'PItn', 'H2O2tn', 'DUDPtn', 'PI5P4Kn', 'PI34P4Pn', 'PI45P3Kn', 'DNADDP', 'DNADtn', 'PIK3n', 'O2Stn', 'PI4P3Kn', 'H2Otn', 'PI3P3Pn', 'PI34P3Pn', 'DUMPtn', 'NICRNTtn', 'PI34P5Kn', 'O2tn', 'PAIL_HStn', 'PI345P5Pn', 'PI3P4Kn', 'MI1P_Dtn', 'ATPtn', 'PIPLCn', 'PI4P5Kn', 'PIK5n']\n", + "Reaction H2Otn is not in Z\n", + "1481\n", + "1481\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 945 (119 core, 826 non-core); Num. remaining: 229\n", + "Reaction no. 752\n", + "Attempting to remove reaction: EX_h2o_e ...\n", + "Initial PM reactions: 1481\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1176680000007764\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CREATt4_2_r', 'GLUt2m'], inactive_NC:['GACMTRc', 'EX_creat_e', 'EX_h2o_e', 'GLYAMDTRc']\n", + "Reaction EX_h2o_e is not in Z\n", + "1481\n", + "1481\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 945 (119 core, 826 non-core); Num. remaining: 228\n", + "Reaction no. 753\n", + "Attempting to remove reaction: ARTCOAL1 ...\n", + "Initial PM reactions: 1481\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 25 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4384319999999207\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 26 , inactive_C: ['PLA2_2', 'LPS3', 'RDH2a', 'LPASE', 'PUNP1', 'RDH1a'], inactive_NC:['EX_retinol_9_cis_e', 'LPS2', 'RETH1e', 'RETH2e', 'RETFAt2', 'RETH1', 'RETH2', 'EX_caro_e', 'RAI2', 'BCDO', 'LRAT1', 'RETFAt1', 'LRAT2', 'CAROtr', 'EX_retinol_cis_11_e', 'LRAT', 'GPDDA1', 'GLYK', 'RETI1', 'ARTCOAL1']\n", + "Reaction ARTCOAL1 is not in Z\n", + "1481\n", + "1481\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 945 (119 core, 826 non-core); Num. remaining: 227\n", + "Reaction no. 754\n", + "Attempting to remove reaction: RETFA ...\n", + "Initial PM reactions: 1481\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3005899999998292\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['RETFA']\n", + "Reaction RETFA is not in Z\n", + "1481\n", + "1481\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1480\n", + "Num. removed: 946 (119 core, 827 non-core); Num. remaining: 226\n", + "Reaction no. 755\n", + "Attempting to remove reaction: 2DR1PP ...\n", + "Initial PM reactions: 1480\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1637659999996686\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['DADAe', 'DADA', 'LEUTAm', 'GLUt2m', 'PUNP6'], inactive_NC:['DINt', 'DRPA', 'DRBK', 'GLYtm', 'LEUt5m', '2DR1PP']\n", + "Reaction 2DR1PP is not in Z\n", + "1480\n", + "1480\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 946 (119 core, 827 non-core); Num. remaining: 225\n", + "Reaction no. 756\n", + "Attempting to remove reaction: KDNH ...\n", + "Initial PM reactions: 1480\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 195 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.7937369999999646\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 196 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'ACNAM9PL2', 'SOAT12', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'GASNASE2ly', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'AHEXASE2ly', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'HEX4', 'MEVK1x', 'A_MANASEly', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'MANtly', 'DM_kdn_c', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'GLCt4', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'B_MANNASEly', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'KDNH', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'ENGASE2ly', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'EX_n2m2nmasn_e', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'N2M2NMASNtly', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'ACGAMtly', 'DM_Asn_X_Ser_Thr_l', 'NDP6', 'COAtp']\n", + "Reaction KDNH is not in Z\n", + "1480\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1480\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 946 (119 core, 827 non-core); Num. remaining: 224\n", + "Reaction no. 757\n", + "Attempting to remove reaction: MI134P4P ...\n", + "Initial PM reactions: 1480\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1074349999998958\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['MI13PP', 'MI134P4P']\n", + "Reaction MI134P4P is not in Z\n", + "1480\n", + "1480\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1478\n", + "Num. removed: 948 (119 core, 829 non-core); Num. remaining: 222\n", + "Reaction no. 758\n", + "Attempting to remove reaction: PAFS ...\n", + "Initial PM reactions: 1478\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4300100000000384\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['FTHFLi', 'MTHFD', 'PAFH', 'PUNP1', 'MTHFC'], inactive_NC:['EX_pi_e', 'PAFS']\n", + "Reaction PAFS is not in Z\n", + "1478\n", + "1478\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 948 (119 core, 829 non-core); Num. remaining: 221\n", + "Reaction no. 759\n", + "Attempting to remove reaction: ARTCOAL2 ...\n", + "Initial PM reactions: 1478\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4473280000001978\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['PLA2_2', 'NKCC2t', 'LPS3'], inactive_NC:['LPS2', 'GLYK', 'ARTCOAL2', 'RETH', 'RETH1', 'RETH2', 'LRAT']\n", + "Reaction ARTCOAL2 is not in Z\n", + "1478\n", + "1478\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 948 (119 core, 829 non-core); Num. remaining: 220\n", + "Reaction no. 760\n", + "Attempting to remove reaction: FADH2tru ...\n", + "Initial PM reactions: 1478\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 93 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4020440000003873\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 94 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'GLCt4', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction FADH2tru is not in Z\n", + "1478\n", + "1478\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 948 (119 core, 829 non-core); Num. remaining: 219\n", + "Reaction no. 761\n", + "Attempting to remove reaction: PGPP_hs ...\n", + "Initial PM reactions: 1478\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 29 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.465422000000217\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 30 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'DCYTD', 'RNDR4'], inactive_NC:['THMDt4', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'PEFLIP', 'NDP6', 'AHCYStr']\n", + "Reaction PGPP_hs is not in Z\n", + "1478\n", + "1478\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 948 (119 core, 829 non-core); Num. remaining: 218\n", + "Reaction no. 762\n", + "Attempting to remove reaction: GUR1PP ...\n", + "Initial PM reactions: 1478\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4269389999999476\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['GLUt2m', 'SERtN1', 'LEUTAm'], inactive_NC:['UDPG1P', 'LEUt5m', 'GUR1PP']\n", + "Reaction GUR1PP is not in Z\n", + "1478\n", + "1478\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 948 (119 core, 829 non-core); Num. remaining: 217\n", + "Reaction no. 763\n", + "Attempting to remove reaction: ACNAMPH ...\n", + "Initial PM reactions: 1478\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1612489999997706\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['ACNAM9PL', 'AMANK'], inactive_NC:['ACNAMPH']\n", + "Reaction ACNAMPH is not in Z\n", + "1478\n", + "1478\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 948 (119 core, 829 non-core); Num. remaining: 216\n", + "Reaction no. 764\n", + "Attempting to remove reaction: FADtru ...\n", + "Initial PM reactions: 1478\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 96 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4140459999998711\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 97 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'PUNP1', 'EBP1r', 'HMGCOARx', 'C4STMO1r', 'MACACI', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'GDHm', 'PSSA2_hs', 'C4STMO2Pr', 'SERtN1', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'GLCt4', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction FADtru is not in Z\n", + "1478\n", + "1478\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 948 (119 core, 829 non-core); Num. remaining: 215\n", + "Reaction no. 765\n", + "Attempting to remove reaction: THMP ...\n", + "Initial PM reactions: 1478\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4556860000002416\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['SERtN1', 'GDHm'], inactive_NC:['THMP', 'TDP']\n", + "Reaction THMP is not in Z\n", + "1478\n", + "1478\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 948 (119 core, 829 non-core); Num. remaining: 214\n", + "Reaction no. 766\n", + "Attempting to remove reaction: PI45P4P ...\n", + "Initial PM reactions: 1478\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4583789999996952\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CREATt4_2_r', 'PUNP1'], inactive_NC:['PI45P4P', 'GACMTRc', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction PI45P4P is not in Z\n", + "1478\n", + "1478\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 948 (119 core, 829 non-core); Num. remaining: 213\n", + "Reaction no. 767\n", + "Attempting to remove reaction: PI4PP ...\n", + "Initial PM reactions: 1478\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1105500000003303\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['PI4PP']\n", + "Reaction PI4PP is not in Z\n", + "1478\n", + "1478\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1477\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 212\n", + "Reaction no. 768\n", + "Attempting to remove reaction: H2Otp ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 52 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2667460000002393\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 53 , inactive_C: ['GCALDD', 'CATp', '2HBO', 'FAOXC161802m', 'C161CPT22', 'FBA4', 'XAOx', 'ALAR', '2HBt2', 'GLYCLTDy', 'DCSPTN1CPT1', 'TRIODTHYt2', 'CAT2p', 'PYRt2p', 'PUNP7', 'DCSPTN1CPT2', 'C161CRN2t', 'C161CPT12', 'FAOXC2252053m', 'GLXO1', 'NTD10', 'FAOXC2251836m', 'XAO2x', 'SPODMx', 'XANDp', 'DCSPTN1CRNt'], inactive_NC:['H2Otp', 'GLYCTO1p', 'PMTCOAtx', 'DESAT22_1p', 'ETOHtx', 'EX_oxa_e', 'GLXtp', 'GUAD', 'DCSPTN1COAtx', 'TRIODTHYt', 'URATEt', 'DALAxt', 'ADRNCOAtx', 'GLYCLTtp', 'DALAOXx', 'ACOAO7p', 'HDD2COAtx', 'URATEtx', 'HXANtx', 'EX_2hb_e', 'NH4tp', 'XANtx', 'O2Stx', 'ARTFR212', 'EX_urate_e', 'KHK2', 'ACALDtx']\n", + "Reaction H2Otp is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 211\n", + "Reaction no. 769\n", + "Attempting to remove reaction: GULN3D ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 210\n", + "Reaction no. 770\n", + "Attempting to remove reaction: XYLTD_D ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 209\n", + "Reaction no. 771\n", + "Attempting to remove reaction: URIDK2m ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.429403000000093\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['DUTPDPm', 'NDPK6'], inactive_NC:['DNDPt41m', 'DNDPt40m', 'DNDPt37m', 'DNDPt38m', 'DNDPt42m', 'URIDK2m', 'DNDPt39m', 'DNDPt43m']\n", + "Reaction URIDK2m is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 208\n", + "Reaction no. 772\n", + "Attempting to remove reaction: AOBUTDsm ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4617030000008526\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['HCO3_CLt'], inactive_NC:['GLYATm', 'AOBUTDsm', 'AACTtm', 'AACTOOR']\n", + "Reaction AOBUTDsm is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 207\n", + "Reaction no. 773\n", + "Attempting to remove reaction: DOLK_L ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 42 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3254029999998238\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 43 , inactive_C: ['THYMDt1', 'RNDR3', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'DCYTD', 'NDPK7', 'RNDR4'], inactive_NC:['DOLPH_Ler', 'HCO3_NAt', 'DNDPt56m', 'CEPTE', 'PA_HSter', 'DM_dctp_m', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'DNDPt55m', 'DOLICHOL_Lter', 'PCHOLPr_hs', 'PGPP_hs', 'DUMPtn', 'DNDPt52m', 'PEFLIP', 'THMDt4', 'biomass_mac', 'DNDPt53m', 'PE_HSter', 'DOLK_L', 'EX_pe_hs_e', 'DNDPt51m', 'DNDPt54m', 'NDP6']\n", + "Reaction DOLK_L is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 206\n", + "Reaction no. 774\n", + "Attempting to remove reaction: RETH1e ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2660219999997935\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['RDH2a'], inactive_NC:['RETFAt1', 'RAI2', 'RETH1e', 'EX_retinol_9_cis_e']\n", + "Reaction RETH1e is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 205\n", + "Reaction no. 775\n", + "Attempting to remove reaction: RETH2e ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4026229999999487\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['HCO3_CLt', 'RDH1a', 'PUNP1'], inactive_NC:['RETI1', 'RETH2e', 'EX_retinol_cis_11_e', 'RETFAt2']\n", + "Reaction RETH2e is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 204\n", + "Reaction no. 776\n", + "Attempting to remove reaction: DOLGPP_Ler ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 49 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4116860000003726\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 50 , inactive_C: ['UDPDOLPT_L', 'THYMDt1', 'RNDR3', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'CREATt4_2_r', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'DCYTD', 'NDPK7', 'RNDR4'], inactive_NC:['DOLPH_Ler', 'DNDPt56m', 'CEPTE', 'PA_HSter', 'GACMTRc', 'DM_dctp_m', 'AHCYStr', 'EX_creat_e', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'DNDPt55m', 'DOLICHOL_Lter', 'PCHOLPr_hs', 'PGPP_hs', 'DOLGPP_Ler', 'DOLP_Lter', 'DUMPtn', 'DOLGLCP_Lter', 'DNDPt52m', 'PEFLIP', 'THMDt4', 'GLYAMDTRc', 'biomass_mac', 'DNDPt53m', 'PE_HSter', 'DOLK_L', 'EX_pe_hs_e', 'DNDPt51m', 'DNDPt54m', 'NDP6']\n", + "Reaction DOLGPP_Ler is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 203\n", + "Reaction no. 777\n", + "Attempting to remove reaction: DOLGPP_Uer ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.562434000000394\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['UDPDOLPT_U', 'CREATt4_2_r'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'DOLGPP_Uer', 'DOLGLCP_Uter', 'DOLP_Uter', 'GACMTRc']\n", + "Reaction DOLGPP_Uer is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 202\n", + "Reaction no. 778\n", + "Attempting to remove reaction: UROLACer ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 201\n", + "Reaction no. 779\n", + "Attempting to remove reaction: GLNLASEer ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 200\n", + "Reaction no. 780\n", + "Attempting to remove reaction: DGULND ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 199\n", + "Reaction no. 781\n", + "Attempting to remove reaction: PHCHGSm ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.143895999999586\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PHCDm', '4HGLSDm'], inactive_NC:['PHCHGSm']\n", + "Reaction PHCHGSm is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 198\n", + "Reaction no. 782\n", + "Attempting to remove reaction: ADPtx ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Model consists of 94 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8325690000001487\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 95 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'LEUTAm', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'LEUt5m', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction ADPtx is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 197\n", + "Reaction no. 783\n", + "Attempting to remove reaction: GLRASE ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 196\n", + "Reaction no. 784\n", + "Attempting to remove reaction: PPItx ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 93 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.63059499999963\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 94 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'PUNP1', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction PPItx is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 195\n", + "Reaction no. 785\n", + "Attempting to remove reaction: GLUt7l ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 53 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5698169999996026\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 54 , inactive_C: ['GGH_7DHFl', 'GGH_5DHFl', 'FPGSm', 'FPGS8', 'FPGS7', 'FPGS6', 'FPGS3', 'FPGS4m', 'GGH_10FTHF5GLUl', 'FPGS9', 'FPGS', 'GLUt2m', 'FPGS5m', 'GGH_10FTHF7GLUl', 'GGH_7THFl', 'FPGS5', 'GGH_5THFl', 'FPGS2', 'FPGS3m', 'FPGS4', 'FPGS7m', 'GGH_6DHFl', 'MTHFCm', 'FPGS2m', 'FPGS8m', 'GGH_10FTHF6GLUl', 'FPGS6m', 'FPGS9m', 'GGH_6THFl'], inactive_NC:['SARCStm', '10FTHF6GLUtl', 'SARDHm', 'THFtm', '7DHFtl', '7DHFtm', '10FTHF7GLUtm', 'DHFtm', '10FTHF6GLUtm', '6THFtl', '5THFtm', '7THFtl', 'GLUt7l', '10FTHF5GLUtl', 'THFtl', '6DHFtm', 'DHFtl', '6DHFtl', 'SARCStex', '10FTHF5GLUtm', '10FTHF7GLUtl', '10FTHFtl', '6THFtm', '7THFtm', 'EX_sarcs_e']\n", + "Reaction GLUt7l is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 194\n", + "Reaction no. 786\n", + "Attempting to remove reaction: EX_gam_e ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.16671899999983\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['HCO3_CLt', 'HEX10', 'GAMt1r'], inactive_NC:['EX_gam_e', 'HCO3_NAt']\n", + "Reaction EX_gam_e is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 193\n", + "Reaction no. 787\n", + "Attempting to remove reaction: ARTFR54 ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4807449999998425\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['FACOAL245_1'], inactive_NC:['ARTFR54', 'TETPENT6t', 'EX_tetpent6_e']\n", + "Reaction ARTFR54 is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 192\n", + "Reaction no. 788\n", + "Attempting to remove reaction: ARTFR56 ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4831560000002355\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['FACOAL244_1'], inactive_NC:['ARTFR56', 'TETTET6t', 'EX_tettet6_e', 'HCO3_NAt']\n", + "Reaction ARTFR56 is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 949 (119 core, 830 non-core); Num. remaining: 191\n", + "Reaction no. 789\n", + "Attempting to remove reaction: ARTFR55 ...\n", + "Initial PM reactions: 1477\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0863730000000942\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['ARTFR55']\n", + "Reaction ARTFR55 is not in Z\n", + "1477\n", + "1477\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1476\n", + "Num. removed: 950 (119 core, 831 non-core); Num. remaining: 190\n", + "Reaction no. 790\n", + "Attempting to remove reaction: ARTFR57 ...\n", + "Initial PM reactions: 1476\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1715540000004694\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['FACOAL245_2', 'DESAT24_1'], inactive_NC:['EX_tetpent3_e', 'ARTFR57', 'TETPENT3t', 'NH4t3r']\n", + "Reaction ARTFR57 is not in Z\n", + "1476\n", + "1476\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 950 (119 core, 831 non-core); Num. remaining: 189\n", + "Reaction no. 791\n", + "Attempting to remove reaction: ARTFR211 ...\n", + "Initial PM reactions: 1476\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4321890000001076\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['FAEL205'], inactive_NC:['ARTFR211']\n", + "Reaction ARTFR211 is not in Z\n", + "1476\n", + "1476\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 950 (119 core, 831 non-core); Num. remaining: 188\n", + "Reaction no. 792\n", + "Attempting to remove reaction: ARTFR53 ...\n", + "Initial PM reactions: 1476\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1150440000001254\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['ARTFR53']\n", + "Reaction ARTFR53 is not in Z\n", + "1476\n", + "1476\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1475\n", + "Num. removed: 951 (119 core, 832 non-core); Num. remaining: 187\n", + "Reaction no. 793\n", + "Attempting to remove reaction: G5SADrm ...\n", + "Initial PM reactions: 1475\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.134621999999581\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['P5CDm', 'GLU5Km', 'G5SDym', 'PUNP1'], inactive_NC:['EX_pi_e', 'G5SADrm']\n", + "Reaction G5SADrm is not in Z\n", + "1475\n", + "1475\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 951 (119 core, 832 non-core); Num. remaining: 186\n", + "Reaction no. 794\n", + "Attempting to remove reaction: ARTFR212 ...\n", + "Initial PM reactions: 1475\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1584720000000743\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['HCO3_CLt'], inactive_NC:['ARTFR212']\n", + "Reaction ARTFR212 is not in Z\n", + "1475\n", + "1475\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 951 (119 core, 832 non-core); Num. remaining: 185\n", + "Reaction no. 795\n", + "Attempting to remove reaction: MI14P4P ...\n", + "Initial PM reactions: 1475\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.393724000000475\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['MI14P4P', 'TRIODTHYt']\n", + "Reaction MI14P4P is not in Z\n", + "1475\n", + "1475\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 951 (119 core, 832 non-core); Num. remaining: 184\n", + "Reaction no. 796\n", + "Attempting to remove reaction: ARTFR209 ...\n", + "Initial PM reactions: 1475\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3848849999994854\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['GLUt2m', 'PUNP1'], inactive_NC:['ARTFR209']\n", + "Reaction ARTFR209 is not in Z\n", + "1475\n", + "1475\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 951 (119 core, 832 non-core); Num. remaining: 183\n", + "Reaction no. 797\n", + "Attempting to remove reaction: ARTFR202 ...\n", + "Initial PM reactions: 1475\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2329970000000685\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['TRIODTHYt2', 'NKCC2t', 'GDHm'], inactive_NC:['ARTFR202', 'TRIODTHYt']\n", + "Reaction ARTFR202 is not in Z\n", + "1475\n", + "1475\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 951 (119 core, 832 non-core); Num. remaining: 182\n", + "Reaction no. 798\n", + "Attempting to remove reaction: ARTFR210 ...\n", + "Initial PM reactions: 1475\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3660999999992782\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['NKCC2t'], inactive_NC:['ARTFR210']\n", + "Reaction ARTFR210 is not in Z\n", + "1475\n", + "1475\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 951 (119 core, 832 non-core); Num. remaining: 181\n", + "Reaction no. 799\n", + "Attempting to remove reaction: ARTFR208 ...\n", + "Initial PM reactions: 1475\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3583380000000034\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['ARTFR208', 'HCO3_NAt']\n", + "Reaction ARTFR208 is not in Z\n", + "1475\n", + "1475\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1473\n", + "Num. removed: 953 (119 core, 834 non-core); Num. remaining: 180\n", + "Reaction no. 800\n", + "Attempting to remove reaction: ARTFR205 ...\n", + "Initial PM reactions: 1473\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2108319999997548\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CREATt4_2_r', 'GDHm'], inactive_NC:['ARTFR205', 'GACMTRc', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction ARTFR205 is not in Z\n", + "1473\n", + "1473\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 953 (119 core, 834 non-core); Num. remaining: 179\n", + "Reaction no. 801\n", + "Attempting to remove reaction: ARTFR203 ...\n", + "Initial PM reactions: 1473\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1473390000001018\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['ARTFR203', 'TRIODTHYt']\n", + "Reaction ARTFR203 is not in Z\n", + "1473\n", + "1473\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 953 (119 core, 834 non-core); Num. remaining: 178\n", + "Reaction no. 802\n", + "Attempting to remove reaction: ARTFR204 ...\n", + "Initial PM reactions: 1473\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3137139999998908\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['ARTFR204']\n", + "Reaction ARTFR204 is not in Z\n", + "1473\n", + "1473\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1472\n", + "Num. removed: 954 (119 core, 835 non-core); Num. remaining: 177\n", + "Reaction no. 803\n", + "Attempting to remove reaction: ARTFR206 ...\n", + "Initial PM reactions: 1472\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3736079999998765\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['ARTFR206']\n", + "Reaction ARTFR206 is not in Z\n", + "1472\n", + "1472\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1471\n", + "Num. removed: 955 (119 core, 836 non-core); Num. remaining: 176\n", + "Reaction no. 804\n", + "Attempting to remove reaction: PI3P4Kn ...\n", + "Initial PM reactions: 1471\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1057810000002064\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['PI3P4Kn']\n", + "Reaction PI3P4Kn is not in Z\n", + "1471\n", + "1471\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1470\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 175\n", + "Reaction no. 805\n", + "Attempting to remove reaction: PIK3n ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1398519999993368\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GDHm'], inactive_NC:['PIK3n']\n", + "Reaction PIK3n is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 174\n", + "Reaction no. 806\n", + "Attempting to remove reaction: PIK4n ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3027489999994941\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GDHm'], inactive_NC:['PIK4n']\n", + "Reaction PIK4n is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 173\n", + "Reaction no. 807\n", + "Attempting to remove reaction: PIK5n ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4309479999992618\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['TRIODTHYt2'], inactive_NC:['EX_pi_e', 'NH4t3r', 'GLYtm', 'PI5P4Kn', 'PIK5n', 'TRIODTHYt']\n", + "Reaction PIK5n is not in Z\n", + "1470\n", + "1470\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 172\n", + "Reaction no. 808\n", + "Attempting to remove reaction: PI4P3Kn ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1733099999992191\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GDHm'], inactive_NC:['PI4P3Kn']\n", + "Reaction PI4P3Kn is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 171\n", + "Reaction no. 809\n", + "Attempting to remove reaction: PHACCOAGLNAC ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3782719999999244\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['PEAMNO', 'ALDD19xr', 'ALDD19x_P'], inactive_NC:['PACCOAL', 'EX_pheacgln_e', 'PHEACGLNt', 'PHACCOAGLNAC', 'PHYCBOXL']\n", + "Reaction PHACCOAGLNAC is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 170\n", + "Reaction no. 810\n", + "Attempting to remove reaction: COAtp ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 99 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.670669000000089\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 100 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'CREATt4_2_r', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'HCO3_CLt', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['EX_pi_e', 'PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'GACMTRc', 'AHCYStr', 'EX_creat_e', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'GLCt4', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'GLYAMDTRc', 'PE_HSter', 'CHSTEROLt2', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction COAtp is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 169\n", + "Reaction no. 811\n", + "Attempting to remove reaction: 3SPYRSPm ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1489649999994072\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['3SALATAim', '3SALAASPm'], inactive_NC:['FUMSO3tm', '3SPYRSPm']\n", + "Reaction 3SPYRSPm is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 168\n", + "Reaction no. 812\n", + "Attempting to remove reaction: ADCim ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.285823000000164\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['LEUTAm', 'ACETONEt2m'], inactive_NC:['ADCim', 'ACTNMO', 'LEUt5m']\n", + "Reaction ADCim is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 167\n", + "Reaction no. 813\n", + "Attempting to remove reaction: OBDHc ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4053389999999126\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['OBDHc', 'TRIODTHYt']\n", + "Reaction OBDHc is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 166\n", + "Reaction no. 814\n", + "Attempting to remove reaction: 3SALAOX ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1458360000005996\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GLCt1'], inactive_NC:['3SALAOX']\n", + "Reaction 3SALAOX is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 165\n", + "Reaction no. 815\n", + "Attempting to remove reaction: Htx ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 144 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.6869659999993019\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 145 , inactive_C: ['GCALDD', 'CATp', 'FAOXC161802m', 'DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'C161CPT22', 'PETOHMr_hs', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'XAOx', 'FUMAC', 'EBP1r', 'PUNP1', 'ALAR', 'HMGCOARx', 'C4STMO1r', 'MACACI', 'RNDR4', 'DCYTD', 'PMEVKx', 'GLYCLTDy', 'DHCR241r', 'THYMDt1', 'DCSPTN1CPT1', 'GDHm', 'PSSA2_hs', 'C4STMO2Pr', 'CAT2p', 'DMATTx', 'SOAT11', 'TYRTA', 'FBA4', 'PYRt2p', 'PUNP7', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DCSPTN1CPT2', 'SQLSr', 'DHCRD2', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'C161CRN2t', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'FAOXC2252053m', 'C14STRr', 'C161CPT12', 'SQLEr', 'GLXO1', 'NTD10', 'NTD3', 'FAOXC2251836m', 'DHCR243r', 'XAO2x', 'IPDDIx', 'SOAT12', 'SPODMx', 'DPMVDx', 'XANDp', 'NDPK6n', 'LSTO1r', 'DHCR71r', 'DCSPTN1CRNt'], inactive_NC:['EX_pi_e', 'H2Otp', 'GLYCTO1p', 'PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'Htx', 'PMTCOAtx', 'GLXtp', 'ETOHtx', 'DESAT22_1p', 'EX_oxa_e', 'GUAD', 'DCSPTN1COAtx', 'AHCYStr', 'URATEt', 'DALAxt', 'EX_thymd_e', 'ADRNCOAtx', 'AMETr', 'GLYCLTtp', 'DUDPtn', 'CHOLtr', 'FADH2tru', 'PCHOLPr_hs', 'PGPP_hs', 'DALAOXx', 'NADPHtxu', 'CO2ter', 'ACOAO7p', 'PROD2', 'HDD2COAtx', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'URATEtx', 'FADtru', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'HXANtx', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'NH4tp', 'XOLTRI25te', 'XANtx', 'O2Stx', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'CHSTEROLt2', 'PE_HSter', 'ARTFR212', 'EX_pe_hs_e', 'EX_urate_e', 'KHK2', 'EX_xolest_hs_e', 'XOLESTte', 'ACALDtx', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction Htx is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 164\n", + "Reaction no. 816\n", + "Attempting to remove reaction: BHBt ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1122 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 3.163536999999451\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1123 , inactive_C: ['C3STDH1Pr', 'CAMPt', 'PETOHMr_hs', 'FPGS7', 'GDHm', 'FAS160COA', 'MI145PK', 'AHCi', 'HPDCACRNt', 'GPAM_hs', 'C161CPT1', 'PI45P5P', 'GLUNm', 'ADRNCPT2', 'MTHFD', 'SQLSr', 'PRFGS', 'GGH_5THFl', 'FMNAT', 'LCYSTAT', 'PCHOLP_hs', 'CBPSam', 'FAOXC204184m', 'GLCAASE9ly', 'NTD2', 'PTDCACRNCPT2', 'GLNS', 'GGH_10FTHF6GLUe', 'XAO2x', 'LNLNCGCPT1', 'ACNAM9PL', 'TTDCPT1', 'FPGS9m', 'CITtbm', 'CYTDK1', 'PEPCKm', 'PGI', 'COAtim', 'MACACI', 'EICOSTETCPT2', 'HOXG', 'PPNCL3', 'DADA', 'FAEL204', 'G6Pter', 'RPI', 'PSP_L', 'CAT2p', 'GF6PTA', 'PI5P4K', 'DCSPTN1CPT2', 'PPA', 'UGLT', 'FATP2t', 'LPASE', 'GGH_5DHFe', 'LNS14DMr', 'RDH1a', 'CTPS2', 'SIAASEly', 'LNELDCCPT1', 'DADAe', 'FAOXC183803m', 'VACCCPT1', 'FAS120COA', 'HMBS', 'HSD17B7r', 'FAOXC2051843m', 'PFK26', 'CHLPCTD', 'ADNK1', 'GGH_7DHFl', 'FACOAL170', 'DESAT24_1', 'CATm', 'FPGSm', 'CYTD', 'PTDCACRNCPT1', 'FATP3t', 'DHCR241r', 'THYMDt1', 'ACITL', 'ORPT', 'RTOTAL2CRNCPT1', 'DLNLCGCPT1', 'FPGS3m', 'FPGS7m', 'LSTO2r', 'FAEL183', 'ACACT1r_copy1', 'FPGS2m', 'MEVK1x', 'A_MANASEly', 'IMPC', 'DESAT18_8', 'PYRt2m', 'TMDPK', '4NPHSULT', 'GLXO1', 'NTD10', 'STRDNCCRNt', 'MI34PP', 'MTAP', 'LNLNCGCPT2', 'PTPATi', 'ALCD2y', 'NTD5', 'DESAT18_4', 'XANDp', 'NDP3ex', 'IMPD', 'FAS80COA_L', 'ACNAMlt', 'MI134PP', 'VALTAim', 'FACOAL1832', 'C3STDH1r', 'DESAT18_9', 'ADNtm', 'GGNG', 'PNTK', 'HSD17B8r', 'PI45P3K', 'BUTt2m', 'GTHS', 'C160CRNt', 'GLGNS1', 'FPGS6', 'FAOXC183806m', 'G6PDH2r', 'DESAT18_6', 'MMMm', 'C161CRNt', 'ACYP', 'FPGS5', 'CPPPGO', 'GGH_6DHFl', 'ECOAH9m', 'ARGNm', 'FAOXC150m', 'BILIRED', 'HSD17B9r', 'PI4PLC', 'CSm', 'G6PDA', 'ORNDC', 'DHCRD1', 'PI3P5K', 'STRDNCCPT1', 'ICDHyr', 'STS4', 'MCLORi', 'FPGS8', 'PI35P3P', 'LYSt4', 'PNP', 'PRGNLONESULT', 'ADPRDP', 'NTP3e', 'EICOSTETCRNt', 'ELAIDCPT1', 'HISt4', 'MI145PP', 'HACD1m', 'KAS8', 'METLEUex', 'GTHOr', 'ESTSULT', 'FUCASEe', 'ALDD19x_P', 'GMPR', 'RTOTALCRNCPT1', 'SOAT12', 'ARGSS', 'CGLYt3_2', 'GGH_10FTHF6GLUl', 'GALUi', 'ACOAD1fm', 'TKT1', 'ADK1', 'ACOAD9m', 'NDPK6n', 'SERPT', 'GTHOm', 'AMPDA', 'DURIK1', 'C161CPT22', 'C161CPT2', 'SMS', 'GRTTx', 'PGPPT', 'TYMSULT', 'XAOx', '24_25VITD2Hm', 'PSERT', 'STS3', 'PI345P5P', 'C181CRNt', 'TRIODTHYt2', 'GLUt2m', 'NTD2e', 'ACACT1m', 'GGH_10FTHF7GLUl', 'GGH_7DHFe', 'OIVD3m', 'METS', 'METAT', 'ACETONEt2m', 'PI345P3P', 'FAOXC1811602m', 'PFK', 'SBPP3er', 'DGNSKm', 'C14STRr', 'FAOXC160', 'DESAT20_2', 'DHPM1', 'RTOTALCRNt', 'LSTO1r', 'XYLUR', 'CDS', 'RTOTAL3CRNCPT1', 'ALASm', 'CRNtim', 'OMPDC', 'ADNCYC', 'DUTPDPn', 'ASNS1', 'LEUTAm', 'PRAGSr', 'AHEXASE2ly', 'FUMAC', 'PUNP6', 'PMEVKx', 'UDPDOLPT_L', 'GGH_6DHFe', 'NTD1', 'PIPLC', '41R1H2MAE12BOOX', 'PI34P5K', 'FAOXC180', 'NTD4', 'MI1345PP', 'GGH_5THFe', 'PIK5', 'URIK1', 'PYNP2r', 'NT5C', 'SQLEr', 'OIVD2m', 'FAOXC2251836m', 'FPGS8m', 'ORNt', 'SFGTHi', 'NTD7', 'AHEXASEly', 'HEX10', 'ACOAD10m', 'HEX1', 'NTD9e', 'FOLR2', 'UGCG', 'PLA2_2', 'NTD8', 'LPS3', 'NDPK8', 'PUNP3', 'DMATTx', 'CYSTS', 'CAATPS', 'LEUt4', 'DHFR', 'GLCAASE8ly', 'FAS140COA', 'PETHCT', 'ASPTAm', 'GASNASEly', 'SUCOAS1m', 'RTOTALCRNCPT2', 'PRASCSi', 'ACS', 'TRPt4', 'HEX7', 'FAOXC2031836m', 'ETHAK', 'UAGDP', 'GGH_6THFl', 'SPODMm', 'PDHm', 'GCALDD', 'ABUTD', 'GMPS2', 'PUNP1', 'ACCOAC', 'PTDCACRNt', 'ECOAH1m', '3SALAASPm', 'NACHEX27ly', 'TMNDNCCRNt', 'TTDCRNt', 'RNDR3', 'PRPPS', 'PIK4', 'TYRTA', 'GGH_7THFl', 'PPPGOm', 'EICOSTETCPT1', 'SULFOX', 'DPGM', 'MI3PP', 'FPGS4', 'DGAT', 'AMANK', 'ACGAMK', 'MI4PP', 'FAOXC18280m', 'ACNAM9PL2', 'AGPAT1', 'TMNDNCCPT2', 'MGCHrm', 'FAOXC170m', 'FAOXC18480m', 'DHCR71r', 'NTD9', 'LNSTLSr', 'GK1', 'ACONT', 'PDE1', 'ECOAH12m', 'NDPK7', 'BUTt2r', 'DCSPTN1CPT1', 'THMt3', 'FPGS5m', 'GGH_10FTHF7GLUe', 'GLCURtly', 'DPCOAK', 'FACOAL161', 'TMDS', 'GLBRAN', 'LYSt5r', 'C181CPT1', 'FACOAL260', 'FACOAL245_1', 'GASNASE2ly', 'PIK3', 'C161CRN2t', 'FAOXC1811603m', '3SALATAim', 'NTD6', 'PGCD', 'GALASE1ly', 'CERT2rt', 'FPGS6m', 'FACOAL1821', 'PEAMNO', 'ME2', 'PROt4', 'VACCCPT2', 'GAMt1r', 'PAFH', 'SALMCOM2', 'GBA', 'AIRCr', 'ACGAM6PS', 'AICART', 'STRDNCCPT2', 'ALDD2x', 'C204CPT1', 'FACOAL181', 'FACOAL241', 'FBP26', 'ACRNtm', 'LNELDCCPT2', 'C180CRNt', 'NDPK1', 'C4STMO2Pr', 'C204CPT2', 'FAOXC16180m', 'LNLNCGCRNt', 'GLPASE1', 'MI1PP', 'HEX4', 'FAOXC182806m', 'C161CPT12', 'SBPP1er', 'UREAt', 'RBFK', 'IPDDIx', 'DPMVDx', 'TMNDNCCPT1', 'SLDx', 'RTOTAL3CRNt', 'PI4P5K', 'UDPDOLPT_U', 'LNLCCPT2', 'FTHFLi', 'LNELDCCRNt', 'GGH_5DHFl', 'OCOAT1m', 'LNLNCACPT2', 'HMGCOARx', 'FPGS4m', 'ILEt4', 'PSSA2_hs', 'ACS2', 'FACOAL180', 'UPP3S', 'CHOLK', 'ADRNCRNt', 'PYDXDH', 'CYSTA', 'PUNP7', 'DESAT18_3', 'CTPS1', 'FPGS2', 'LNLCCPT1', 'NTD4e', 'FACOAL150', 'DESAT18_5', 'FAOXC80', 'CDIPTr', 'C160CPT1', 'DHCR243r', 'ARGSL', 'FAOXC204', '24_25VITD3Hm', 'PI45PLC', 'MI14PP', 'FALDH', 'NDPK2', 'AMPTASECG', 'FAS100COA', 'GGH_10FTHF5GLUe', 'DLNLCGCRNt', 'EBP2r', 'C160CPT2', 'EBP1r', 'ADSL1r', 'FACOAL204_copy2', 'NTD11', 'SUCD1m', 'GGH_6THFe', 'PPCDC', 'SOAT11', 'ADMDC', 'OIVD1m', 'VALt4', 'CERK', 'ALDD2xm', 'ALDD2y', 'FACOAL244_1', 'CERT1rt', 'RTOTAL2CRNCPT2', 'FACOAL80', 'BTNt2i', 'C4STMO2r', 'GUACYC', 'MTHFCm', 'ETF', 'FAOXC2252053m', 'C180CPT2', 'CGMPt', 'ADRNCPT1', 'TALA', 'GTHPm', 'SPODMn', 'MCPST', 'CITtam', 'METt4', 'BAMPPALDOX', 'FAOXC161802m', 'CHSTEROLSULT', 'CYSTGLUex', 'DLNLCGCPT2', 'NMNATn', 'HIBDm', 'SADT', 'C4STMO1r', 'RNDR4', 'TKT2', 'PROSTGE1t3', 'GARFT', 'ALDD19xr', 'FAS180COA', 'FPGS9', 'UPPDC1', 'RTOTAL2CRNt', 'FACOAL140', 'AACOAT', 'NDP7ex', '5MTHFt', 'FAOXC2242046m', 'PI4P3K', 'SPRMS', 'GLPASE2', 'PRAIS', 'NaKt', 'UAG2EMA', 'UDPGD', 'HMGCOAS', '3DSPHR', 'ACCOAL', 'AMPTASECGe', 'RNDR1', 'ADSL2r', 'DCSPTN1CRNt', 'DESAT18_10', 'ARGt4', 'FAOXC140', 'DPGase', 'FAEL184', 'VACCCRNt', 'NNATn', 'DCYTD', 'MTHFC', 'STS2', 'GLUPRT', 'THMTP', 'FPGS3', 'ALCD2x', 'PUNP5', 'HMGLm', 'MMEm', 'CREATt4_2_r', 'PI3PP', 'PROSTGE2t3', 'FAOXC16080m', 'H2CO3D', 'PI345P3Pn', 'HACD9m', 'DHCR72r', 'FACOAL160', 'ADSS', 'ACGAMPM', 'TMDK1', 'NTD3', 'ELAIDCRNt', 'DAGKn_hs', 'HPDCACRNCPT1', 'ADPT', 'STS1', 'GLDBRAN', 'RTOTAL3CRNCPT2', 'DGK1', 'NDP8ex', 'FBA4', 'GGH_7THFe', 'FAEL205', 'GALKr', 'ARGLYSex', 'FAOXC1811601m', 'DOPASULT', 'HPDCACRNCPT2', 'SPMS', 'GGH_10FTHF5GLUl', 'TTDCPT2', 'DESAT20_1', 'LNLNCACRNt', 'PI3P4K', 'FACOAL245_2', 'FPGS', 'PI5P3K', 'ADSK', 'DHCR242r', 'DHCRD2', 'LNLCCRNt', 'RNDR2', 'DESAT18_7', '3SALATAi', 'ADK1m', 'C180CPT1', 'LNLNCACPT1', 'C181CPT2', 'ELAIDCPT2', 'RDH2a', 'ARGt5r'], inactive_NC:['24_25DHVITD3t', '7DHFtm', 'P4501B1r', 'EX_hestratriol_e', 'PCHOLPr_hs', 'EX_caro_e', 'DNDPt7m', 'H2Otn', 'GLCURter', 'L_LACDcm', 'PI3P3Pn', 'THMP', 'EX_25hvitd2_e', 'NICRNTtn', 'EX_gtp_e', 'DGK2m', 'FACOAL40im', 'PEFLIP', 'PI345P5Pn', 'EX_but_e', 'DNDPt53m', '10FTHFtl', 'ARTPLM2m', 'UNK3', 'DNDPt57m', 'VITD3Hm', 'ACGAM2E', 'OBDHc', 'DNDPt20m', '7DHFtl', 'CYOR_u10m', 'CYSO', 'DM_dctp_m', 'LEUTA', 'LNLCt', 'ACP1_FMN', 'BALAVECSEC', 'EX_pnto__R_e', 'HSD3A1r', 'BHBt', 'ARTFR52', 'GULN3D', 'PROSTGE2t', 'NADN', 'EX_nrvnc_e', 'GALtly', 'PPAtr', 'HMGCOAtx', 'TCHOLAt3', 'SARCStex', 'O2tm', 'EX_dad_2_e', 'FTHFDH', 'B_MANNASEly', 'CYANt', 'EX_2mcit_e', 'HESTRATRIOLte', 'PPAP', 'ACACT10m', 'ASNNm', 'DOLK_L', 'DNDPt12m', 'EX_fol_e', 'EX_utp_e', 'PI4P5Kn', 'EX_mercplaccys_e', 'EX_ttdca_e', 'OCBTm', 'DNDPt56m', 'EX_tetpent3_e', 'PA_HSter', 'AKGDm', 'PMTCOAtx', 'COt', 'TTDCAtr', 'RETFAt2', 'PIK4n', 'EX_gam_e', 'GUR1PP', 'DNADDP', 'DNADtn', 'DNDPt58m', 'EX_10fthf7glu_e', 'OCCOAtm', 'URATEtx', 'ASPCT', 'MEOHtly', 'FADDP', 'DNDPt52m', 'NMNAT', 'OCTAt', 'LRAT', 'ARTFR56', 'DNDPt43m', 'DM_sprm_c', 'DRPA', 'PHACCOAGLNAC', 'EX_pro__L_e', 'RTOT_3', 'DADNt4', 'EX_hexc_e', 'EX_n2m2nmasn_e', 'NADPtru', 'LPS2', 'HAS2', '10FTHF6GLUtl', 'EX_dhf_e', 'MALSO4tm', 'EX_lnlc_e', '5THFtm', 'EX_ppa_e', 'GLUt7l', 'EX_thymd_e', 'EX_pydx_e', 'MCCCrm', 'S2L2N2M2MASNtly', 'GCHOLAt3', 'ACCOALm', 'TYMSFt', 'FADtru', 'XYLK', 'G6PPer', 'CAROtr', 'PYDXtr', 'DADNK', '24_25DHVITD3tm', 'SPHGNtr', 'UNK2', 'BPNT', 'ACGAMtly', 'ACNAMPH', 'FALDtly', '2DR1PP', 'ENGASEly', 'PPAer', 'EX_xoltri25_e', 'CYSGLTH', 'RETH1e', 'PIter', 'MAOX', 'ETOHMO', 'H2O2tn', 'ARTFR46', 'UPPN', 'EX_octa_e', 'AACTtm', 'ACOAO7p', 'FOLt2', 'GHMT2r', 'DNDPt13m', 'PI34P3Pn', 'HPDCAt', 'MI14P4P', 'SLDt', 'PHEMEtm', 'GULNter', 'DNDPt21m', 'UDPGLCter', 'PPItx', 'HISTAVESSEC', 'HSD3B2r', 'EX_3aib_e', 'EX_xolest_hs_e', 'ETHP', 'XOLESTte', 'CO2tp', 'BILIRUBt2', 'EX_hpdca_e', 'MANtly', 'DM_kdn_c', 'EX_pheacgln_e', 'CHOLATEt3', 'EX_camp_e', 'EX_estrones_e', 'EX_val__L_e', 'ACALDtm', 'EX_tetpent6_e', 'C204CRNt', '3SPYRSPm', 'GLCt4', 'DNDPt30m', 'NADHtru', 'PTRCOX1', 'TETTET6t', '25HVITD2tin', 'ACOAH', 'RETFAt1', 'EX_35cgmp_e', 'CYTDt5', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'PAIL_HStn', 'ESTRONEtr', 'SPHS1Ptr', '3MOPt2im', '6THFtm', 'ARTCOAL1', 'EX_thf_e', 'MCD', 'ACTNMO', 'GND', 'NMNS', 'SARDHm', 'EX_his__L_e', 'DHEASULT', 'GGLUCT', 'DNDPt42m', 'PGPP_hs', 'DM_datp_m', 'DM_dgtp_n', 'PIK3n', 'GLUt6', 'ARTPLM1m', 'ENGASE2ly', 'CYSTSERex', 'GLRASE', 'UDPG1P', 'HGNTOR', 'FORtr', 'THFtl', '6DHFtl', 'DNDPt5m', 'HSD3B3r', 'NADtru', 'PI45P4P', 'ATPasel', '10FTHF7GLUtl', 'THMDt4', 'EX_4nphsf_e', 'PE_HSter', 'ARTFR212', 'EX_pe_hs_e', '3SALAOX', 'ACALDtx', 'O2ter', 'DURAD', 'HIStiDF', 'EX_etoh_e', 'EX_retinol_9_cis_e', 'DRBK', 'EX_cysi__L_e', 'NICRNS', 'FBP', 'PAFS', 'URATEt', 'PPAtm', 'SPHK21c', '4PYRDX', 'DOLGPP_Ler', 'ARTFR203', 'DOLGLCP_Lter', 'NACASPAH', 'GLACter', 'ESTRONESt2', 'EX_mepi_e', 'RNMK', 'EX_ocdca_e', 'URIt5', 'DNDPt18m', 'PIK5n', 'RTOT_2', 'MCLACCYSR', 'CSNATr', 'CYSTGL', 'PA_HStn', 'EX_tcynt_e', 'PGL', 'EX_orn_e', 'PROSTGE1t', 'DOLGLCP_Uter', 'RTOT2', 'SLCBK1', 'DOLP_Uter', 'THFtm', 'EX_ile__L_e', 'MI1PS', 'EX_urea_e', 'DCSPTN1COAtx', 'ADRNCOAtx', 'GLUVESSEC', 'EX_tettet6_e', 'ARTFR45', 'DKMPPD', 'BTNDe', '24_25DHVITD2tm', 'DSAT', 'GLYATm', 'LRAT1', '2MCITt', 'ILETA', 'GCHOLAt2', 'C3STKR2r', '6DHFtm', 'NORANMT', 'DHFtl', 'PDE4', 'DUMPtn', 'CH25H', 'PItx', 'TDP', '3AIBt', 'EX_ocdcea_e', 'DHORD9', 'EX_10fthf_e', 'UDPGNP', 'PNTOt5', 'MI1P_Dtn', '7THFtm', 'DNDPt51m', 'MMTSADm', 'PPPG9tm', 'DHORTS', 'MEPIVESSte', 'AGDC', 'NADPtxu', 'BHBtm', 'GACMTRc', '6THFtl', 'AACTOOR', 'EX_lnlnca_e', 'EX_leu__L_e', 'DUDPtn', 'GLYtm', 'PPBNGS', 'RETH2', 'EX_ptdca_e', 'EX_btn_e', '24_25DHVITD2t', 'CRMPte', 'SPH1Pter', 'NCKt', 'RETH', 'EX_4nph_e', 'EX_2425dhvitd2_e', 'H2CO3D2', 'SPMDOX', '3HBCOAHLm', 'PHYCBOXL', 'XOLTRI25te', 'ASNtm', 'ARTFR54', 'P4507B11r', 'PPAn', 'BDHm', 'FUMSO4tm', 'KDNH', 'UREAtm', 'NADtn', '10FTHF6GLUtm', 'TRIODTHYt', 'PI45P5Pn', '7THFtl', 'EX_thm_e', 'BTNt3i', 'EX_ala_B_e', 'EX_4pyrdx_e', 'CHOLATEt2', 'GTMLTe', 'HISTAtu', 'FDH', 'CO2ter', 'BCDO', 'PROD2', 'HDD2COAtx', '10FTHF5GLUtl', 'ACOAD8m', 'CEPTC', 'HXANtx', 'O2tn', '3AIBTm', 'GPDDA1', 'DNDPt4m', 'EX_thmtp_e', 'GLYK', 'EX_bilirub_e', 'DNDPt31m', 'VALt5m', 'HAS1', 'ARTPLM3m', 'EX_met__L_e', 'PTDCAt', 'DOLGPP_Uer', 'TETPENT6t', 'NADPHtru', 'EX_dopasf_e', 'EX_oxa_e', 'GUAD', 'ARTFR202', 'OPAH', 'HAtly', 'DNDPt3m', 'PItn', 'PRDXl', 'PI5P4Kn', 'RETH1', 'DOLICHOL_Lter', 'O2Stn', 'DGTPtn', 'CBPS', 'PI4P3Kn', 'UROLACer', 'TCHOLAt2', 'ARTFR13', 'TRDR', 'EX_2425dhvitd3_e', 'ARTFR42', 'DGSNtm', 'LNLNCAt', 'XANtx', 'GLUCYS', 'EX_co_e', 'EX_4abut_e', 'MERCPLACCYSt', 'EX_cmp_e', 'GABAVESSEC', 'EX_arg__L_e', 'NDP6', 'COAtp', 'TMDPPK', 'H2O2tly', 'DINt', 'ADNK1m', 'EX_crmp_hs_e', 'NDP7er', 'NMNtn', 'CSNATm', 'ETOHtx', 'DHFtm', 'EX_cyan_e', 'SPHINGStr', 'PACCOAL', 'EX_trp__L_e', 'DGULND', 'DNDPt2m', 'XYLTD_D', 'FCLTm', '4MOPt2im', 'ASPNATm', 'UDPG4E', 'EX_7dhf_e', '4NPHte', 'TETPENT3t', 'ACNML', 'DPCOAPP', 'PIPLCn', 'FATP9t', 'ETOHt', 'GUAPRT', '10FTHF7GLUtm', 'EX_creat_e', 'ARTFR205', 'PI34P4Pn', 'SERHL', 'RTOT5', 'RAI2', '3SPYRSP', 'ARTFR57', 'CITRtm', 'HEXCt', 'MGSA2', 'DNDPt6m', 'FRDPtr', 'ARTFR211', 'EX_bhb_e', 'AOBUTDsm', 'ACSm', 'HKt', 'MTRI', 'TCYNTt', 'XOLTRI25tc', 'SARCStm', '13DAMPPOX', 'ARTFR210', 'ARTFR209', 'EX_sl__L_e', 'MCITS', 'PI4P4Pn', 'HESTRATRIOLtr', 'PHEACGLNt', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'MDRPD', 'PI45P3Kn', 'NADPHtxu', '4NPHSFte', 'EX_biocyt_e', 'DOLP_Lter', 'ADPtx', 'LRAT2', 'PROD2m', 'VBOF', 'PI34P5Kn', 'GLNtm', 'CLOHtex2', '10FTHF5GLUtm', 'ARGtm', 'EX_vitd3_e', '34HPPOR', 'DNDPt19m', 'biomass_mac', 'ADCim', 'GSNt4', 'DNDPt54m', 'KHK2', 'EX_sarcs_e', 'DNDPt32m', 'DNDPt1m', 'ETFQO', 'FE2tm', 'MMSAD1m', 'DOLPH_Ler', 'CEPTE', 'GLNLASEer', 'RETH2e', 'DESAT22_1p', 'AHCYStr', 'FUMSO3tm', 'NACASPtm', '5AOPtm', 'AMETr', 'DOPASFt', 'GLCMter', 'PIt2m', 'ARTCOAL2', 'EX_7thf_e', 'N2M2NMASNtly', '3AIBtm', 'EX_5mthf_e', 'EX_retinol_cis_11_e', 'CYTDt4', 'LEUt5m', 'GLYAMDTRc', 'CHSTEROLt2', 'GULLACter', '2AMACSULT', 'EX_urate_e', 'ATPtn', 'EX_tymsf_e', 'RETI1', 'CYOOm3', 'ARTFR43', 'DM_Asn_X_Ser_Thr_l', 'INOSTO', 'THMTPt']\n", + "Reaction BHBt is not in Z\n", + "1470\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 163\n", + "Reaction no. 817\n", + "Attempting to remove reaction: PI34P5Kn ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4200240000000122\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GDHm'], inactive_NC:['PI34P5Kn']\n", + "Reaction PI34P5Kn is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 956 (119 core, 837 non-core); Num. remaining: 162\n", + "Reaction no. 818\n", + "Attempting to remove reaction: PI5P4Kn ...\n", + "Initial PM reactions: 1470\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1372289999999339\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['PIK5n', 'PI5P4Kn']\n", + "Reaction PI5P4Kn is not in Z\n", + "1470\n", + "1470\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1468\n", + "Num. removed: 958 (119 core, 839 non-core); Num. remaining: 161\n", + "Reaction no. 819\n", + "Attempting to remove reaction: PI45P3Kn ...\n", + "Initial PM reactions: 1468\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0788880000000063\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['PI45P3Kn']\n", + "Reaction PI45P3Kn is not in Z\n", + "1468\n", + "1468\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1467\n", + "Num. removed: 959 (119 core, 840 non-core); Num. remaining: 160\n", + "Reaction no. 820\n", + "Attempting to remove reaction: PI4P5Kn ...\n", + "Initial PM reactions: 1467\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.26357199999984\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['PI4P5Kn']\n", + "Reaction PI4P5Kn is not in Z\n", + "1467\n", + "1467\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1466\n", + "Num. removed: 960 (119 core, 841 non-core); Num. remaining: 159\n", + "Reaction no. 821\n", + "Attempting to remove reaction: HCO3Em ...\n", + "Initial PM reactions: 1466\n", + "check_model_function done ....\n", + "Num. removed: 960 (119 core, 841 non-core); Num. remaining: 158\n", + "Reaction no. 822\n", + "Attempting to remove reaction: MCLACCYSR ...\n", + "Initial PM reactions: 1466\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1508850000000166\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['MCLORi', 'PUNP1'], inactive_NC:['MERCPLACCYSt', 'MCLACCYSR', 'EX_mercplaccys_e']\n", + "Reaction MCLACCYSR is not in Z\n", + "1466\n", + "1466\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 960 (119 core, 841 non-core); Num. remaining: 157\n", + "Reaction no. 823\n", + "Attempting to remove reaction: MGSA2 ...\n", + "Initial PM reactions: 1466\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1515670000007958\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['TRIODTHYt2', 'NKCC2t', 'GDHm'], inactive_NC:['MGSA2', 'TRIODTHYt']\n", + "Reaction MGSA2 is not in Z\n", + "1466\n", + "1466\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 960 (119 core, 841 non-core); Num. remaining: 156\n", + "Reaction no. 824\n", + "Attempting to remove reaction: ATPtx ...\n", + "Initial PM reactions: 1466\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 99 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.655123000000458\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 100 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'PSSA2_hs', 'CREATt4_2_r', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'HCO3_CLt', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['EX_pi_e', 'PPAer', 'EX_xoltri25_e', 'P4507B11r', 'NADPtxu', 'CEPTE', 'PA_HSter', 'GACMTRc', 'AHCYStr', 'EX_creat_e', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'GLCt4', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CH25H', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'XOLTRI25te', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'GLYAMDTRc', 'PE_HSter', 'CHSTEROLt2', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'XOLTRI25tc', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction ATPtx is not in Z\n", + "1466\n", + "1466\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 960 (119 core, 841 non-core); Num. remaining: 155\n", + "Reaction no. 825\n", + "Attempting to remove reaction: NMNS ...\n", + "Initial PM reactions: 1466\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3933280000001105\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['NMNAT', 'NMNS']\n", + "Reaction NMNS is not in Z\n", + "1466\n", + "1466\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1464\n", + "Num. removed: 962 (119 core, 843 non-core); Num. remaining: 154\n", + "Reaction no. 826\n", + "Attempting to remove reaction: UDPG1P ...\n", + "Initial PM reactions: 1464\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0968689999999697\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PUNP1'], inactive_NC:['UDPG1P', 'GUR1PP']\n", + "Reaction UDPG1P is not in Z\n", + "1464\n", + "1464\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 962 (119 core, 843 non-core); Num. remaining: 153\n", + "Reaction no. 827\n", + "Attempting to remove reaction: RETH1 ...\n", + "Initial PM reactions: 1464\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4178179999998974\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['TRIODTHYt2'], inactive_NC:['EX_pi_e', 'RETH1', 'TRIODTHYt']\n", + "Reaction RETH1 is not in Z\n", + "1464\n", + "1464\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 962 (119 core, 843 non-core); Num. remaining: 152\n", + "Reaction no. 828\n", + "Attempting to remove reaction: RETH2 ...\n", + "Initial PM reactions: 1464\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3081099999999424\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['RETH2']\n", + "Reaction RETH2 is not in Z\n", + "1464\n", + "1464\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1463\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 151\n", + "Reaction no. 829\n", + "Attempting to remove reaction: NADN ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1721719999995912\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['NMNATn', 'PNP', 'ADPRDP'], inactive_NC:['RNMK', 'NADtn', 'NADN', 'NMNtn']\n", + "Reaction NADN is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 150\n", + "Reaction no. 830\n", + "Attempting to remove reaction: MGSA ...\n", + "Initial PM reactions: 1463\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4275980000002164\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['TRIODTHYt', 'MGSA']\n", + "Reaction MGSA is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 149\n", + "Reaction no. 831\n", + "Attempting to remove reaction: ASCBOX ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4240460000000894\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['TRIODTHYt2', 'NKCC2t', 'GDHm'], inactive_NC:['ASCBOX', 'TRIODTHYt']\n", + "Reaction ASCBOX is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 148\n", + "Reaction no. 832\n", + "Attempting to remove reaction: H2CO3D2 ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 147\n", + "Reaction no. 833\n", + "Attempting to remove reaction: ADNK1m ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 18 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.103559000000132\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 19 , inactive_C: ['ADNtm'], inactive_NC:['DNDPt13m', 'DNDPt56m', 'ADNK1m', 'DNDPt20m', 'DNDPt21m', 'DNDPt43m', 'DNDPt19m', 'DNDPt18m', 'DNDPt42m', 'DNDPt2m', 'DNDPt30m', 'DNDPt55m', 'DNDPt12m', 'DNDPt31m', 'DNDPt57m', 'DNDPt32m', 'DNDPt58m', 'DNDPt1m']\n", + "Reaction ADNK1m is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 146\n", + "Reaction no. 834\n", + "Attempting to remove reaction: 3SPYRSP ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4432489999999234\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['3SALATAi'], inactive_NC:['3SPYRSP']\n", + "Reaction 3SPYRSP is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 145\n", + "Reaction no. 835\n", + "Attempting to remove reaction: NICRNS ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1293519999999262\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['NT5C'], inactive_NC:['NICRNS']\n", + "Reaction NICRNS is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 144\n", + "Reaction no. 836\n", + "Attempting to remove reaction: DADNK ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 32 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3430340000004435\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 33 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'PUNP1', 'DGAT', 'DCYTD', 'RNDR4', 'NTD6'], inactive_NC:['THMDt4', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'DADNK', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'PEFLIP', 'NDP6', 'AHCYStr']\n", + "Reaction DADNK is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 143\n", + "Reaction no. 837\n", + "Attempting to remove reaction: UDPGNP ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1500669999995807\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['PUNP1'], inactive_NC:['UDPGNP']\n", + "Reaction UDPGNP is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 142\n", + "Reaction no. 838\n", + "Attempting to remove reaction: TDP ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3891329999996742\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GLUt2m', 'TRIODTHYt2'], inactive_NC:['THMP', 'TDP', 'TRIODTHYt']\n", + "Reaction TDP is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 141\n", + "Reaction no. 839\n", + "Attempting to remove reaction: FACOAL226_copy2 ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4299339999997756\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['FACOAL226_copy1'], inactive_NC:['FACOAL226_copy2']\n", + "Reaction FACOAL226_copy2 is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 140\n", + "Reaction no. 840\n", + "Attempting to remove reaction: DHPR2 ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.118123999999625\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PUNP1'], inactive_NC:['NH4t3r', 'DHPR2']\n", + "Reaction DHPR2 is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 139\n", + "Reaction no. 841\n", + "Attempting to remove reaction: PACCOAL ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.417605000000549\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['PEAMNO', 'ALDD19xr', 'ALDD19x_P'], inactive_NC:['PACCOAL', 'EX_pheacgln_e', 'PHEACGLNt', 'PHACCOAGLNAC', 'PHYCBOXL']\n", + "Reaction PACCOAL is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 138\n", + "Reaction no. 842\n", + "Attempting to remove reaction: ENGASE2ly ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.476278000000093\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['AHEXASE2ly', 'GASNASE2ly'], inactive_NC:['EX_n2m2nmasn_e', 'N2M2NMASNtly', 'ENGASE2ly']\n", + "Reaction ENGASE2ly is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 137\n", + "Reaction no. 843\n", + "Attempting to remove reaction: ENGASEly ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 181 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.5808790000000954\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 182 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'SOAT12', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'MEVK1x', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'EX_xoltri25_e', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'CH25H', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'GLCt4', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'XOLTRI25tc', 'XOLTRI25te', 'DNDPt56m', 'P4507B11r', 'PA_HSter', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'NDP6', 'COAtp']\n", + "Reaction ENGASEly is not in Z\n", + "1463\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 136\n", + "Reaction no. 844\n", + "Attempting to remove reaction: GPDDA1 ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 21 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2534540000006018\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 22 , inactive_C: ['PLA2_2', 'RDH2a', 'LPASE', 'PUNP1', 'RDH1a'], inactive_NC:['BCDO', 'RETFAt1', 'GPDDA1', 'EX_retinol_9_cis_e', 'LRAT2', 'LRAT', 'RETH1e', 'RETH', 'RETH1', 'CAROtr', 'RETI1', 'RETH2e', 'EX_retinol_cis_11_e', 'LRAT1', 'EX_caro_e', 'RAI2', 'RETFAt2']\n", + "Reaction GPDDA1 is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 135\n", + "Reaction no. 845\n", + "Attempting to remove reaction: DKMPPD ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 16 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4422230000000127\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 17 , inactive_C: ['SPMS', 'MTAP', 'CREATt4_2_r', 'SPRMS', 'BAMPPALDOX', 'ADMDC'], inactive_NC:['DM_sprm_c', 'EX_creat_e', 'GLYAMDTRc', '13DAMPPOX', 'UNK2', 'UNK3', 'SPMDOX', 'MDRPD', 'GACMTRc', 'MTRI', 'DKMPPD']\n", + "Reaction DKMPPD is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 134\n", + "Reaction no. 846\n", + "Attempting to remove reaction: ATPtn ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 15 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4806500000004235\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 16 , inactive_C: ['NKCC2t', 'GDHm', 'ADPRDP', 'TRIODTHYt2', 'NMNATn', 'NNATn', 'PNP'], inactive_NC:['DNADDP', 'NICRNTtn', 'ATPtn', 'NADN', 'NMNtn', 'RNMK', 'DNADtn', 'NADtn', 'TRIODTHYt']\n", + "Reaction ATPtn is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 133\n", + "Reaction no. 847\n", + "Attempting to remove reaction: UNK2 ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1044809999993959\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['TRIODTHYt2', 'NKCC2t', 'GDHm'], inactive_NC:['UNK2', 'TRIODTHYt']\n", + "Reaction UNK2 is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 132\n", + "Reaction no. 848\n", + "Attempting to remove reaction: DPCOAPP ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4629299999996874\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['DPCOAPP', 'TRIODTHYt']\n", + "Reaction DPCOAPP is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 131\n", + "Reaction no. 849\n", + "Attempting to remove reaction: FE2tm ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 130\n", + "Reaction no. 850\n", + "Attempting to remove reaction: BHBtm ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1112 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 3.912882000000536\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1113 , inactive_C: ['C3STDH1Pr', 'CAMPt', 'PETOHMr_hs', 'FPGS7', 'GDHm', 'FAS160COA', 'MI145PK', 'AHCi', 'HPDCACRNt', 'GPAM_hs', 'C161CPT1', 'PI45P5P', 'GLUNm', 'ADRNCPT2', 'MTHFD', 'SQLSr', 'PRFGS', 'GGH_5THFl', 'FMNAT', 'LCYSTAT', 'PCHOLP_hs', 'CBPSam', 'FAOXC204184m', 'GLCAASE9ly', 'NTD2', 'PTDCACRNCPT2', 'GLNS', 'GGH_10FTHF6GLUe', 'XAO2x', 'LNLNCGCPT1', 'ACNAM9PL', 'TTDCPT1', 'FPGS9m', 'CITtbm', 'CYTDK1', 'PEPCKm', 'PGI', 'COAtim', 'MACACI', 'EICOSTETCPT2', 'HOXG', 'PPNCL3', 'DADA', 'FAEL204', 'G6Pter', 'RPI', 'PSP_L', 'CAT2p', 'GF6PTA', 'PI5P4K', 'DCSPTN1CPT2', 'PPA', 'UGLT', 'FATP2t', 'LPASE', 'GGH_5DHFe', 'LNS14DMr', 'RDH1a', 'CTPS2', 'SIAASEly', 'LNELDCCPT1', 'DADAe', 'FAOXC183803m', 'VACCCPT1', 'FAS120COA', 'HMBS', 'HSD17B7r', 'FAOXC2051843m', 'PFK26', 'CHLPCTD', 'ADNK1', 'GGH_7DHFl', 'FACOAL170', 'DESAT24_1', 'CATm', 'FPGSm', 'CYTD', 'PTDCACRNCPT1', 'FATP3t', 'DHCR241r', 'THYMDt1', 'ACITL', 'ORPT', 'RTOTAL2CRNCPT1', 'DLNLCGCPT1', 'FPGS3m', 'FPGS7m', 'LSTO2r', 'FAEL183', 'ACACT1r_copy1', 'FPGS2m', 'MEVK1x', 'A_MANASEly', 'IMPC', 'DESAT18_8', 'PYRt2m', 'TMDPK', '4NPHSULT', 'GLXO1', 'NTD10', 'STRDNCCRNt', 'MI34PP', 'MTAP', 'LNLNCGCPT2', 'PTPATi', 'ALCD2y', 'NTD5', 'DESAT18_4', 'XANDp', 'NDP3ex', 'IMPD', 'FAS80COA_L', 'ACNAMlt', 'MI134PP', 'VALTAim', 'FACOAL1832', 'C3STDH1r', 'DESAT18_9', 'ADNtm', 'GGNG', 'PNTK', 'HSD17B8r', 'PI45P3K', 'BUTt2m', 'GTHS', 'C160CRNt', 'GLGNS1', 'FPGS6', 'FAOXC183806m', 'G6PDH2r', 'DESAT18_6', 'MMMm', 'C161CRNt', 'ACYP', 'FPGS5', 'CPPPGO', 'GGH_6DHFl', 'ECOAH9m', 'ARGNm', 'FAOXC150m', 'BILIRED', 'HSD17B9r', 'PI4PLC', 'CSm', 'G6PDA', 'ORNDC', 'DHCRD1', 'PI3P5K', 'STRDNCCPT1', 'ICDHyr', 'STS4', 'MCLORi', 'FPGS8', 'PI35P3P', 'LYSt4', 'PNP', 'PRGNLONESULT', 'ADPRDP', 'NTP3e', 'EICOSTETCRNt', 'ELAIDCPT1', 'HISt4', 'MI145PP', 'HACD1m', 'KAS8', 'METLEUex', 'GTHOr', 'ESTSULT', 'FUCASEe', 'ALDD19x_P', 'GMPR', 'RTOTALCRNCPT1', 'SOAT12', 'ARGSS', 'CGLYt3_2', 'GGH_10FTHF6GLUl', 'GALUi', 'ACOAD1fm', 'TKT1', 'ADK1', 'ACOAD9m', 'NDPK6n', 'SERPT', 'GTHOm', 'AMPDA', 'DURIK1', 'C161CPT22', 'C161CPT2', 'SMS', 'GRTTx', 'PGPPT', 'TYMSULT', 'XAOx', '24_25VITD2Hm', 'PSERT', 'STS3', 'PI345P5P', 'C181CRNt', 'GLUt2m', 'NTD2e', 'ACACT1m', 'GGH_10FTHF7GLUl', 'GGH_7DHFe', 'OIVD3m', 'METS', 'METAT', 'ACETONEt2m', 'PI345P3P', 'FAOXC1811602m', 'PFK', 'SBPP3er', 'DGNSKm', 'C14STRr', 'FAOXC160', 'DESAT20_2', 'DHPM1', 'RTOTALCRNt', 'LSTO1r', 'XYLUR', 'CDS', 'RTOTAL3CRNCPT1', 'ALASm', 'CRNtim', 'OMPDC', 'ADNCYC', 'DUTPDPn', 'ASNS1', 'LEUTAm', 'PRAGSr', 'AHEXASE2ly', 'FUMAC', 'PUNP6', 'PMEVKx', 'UDPDOLPT_L', 'GGH_6DHFe', 'NTD1', 'PIPLC', '41R1H2MAE12BOOX', 'PI34P5K', 'FAOXC180', 'NTD4', 'MI1345PP', 'GGH_5THFe', 'PIK5', 'URIK1', 'PYNP2r', 'NT5C', 'SQLEr', 'OIVD2m', 'FAOXC2251836m', 'FPGS8m', 'ORNt', 'SFGTHi', 'NTD7', 'AHEXASEly', 'HEX10', 'ACOAD10m', 'HEX1', 'NTD9e', 'FOLR2', 'UGCG', 'PLA2_2', 'NTD8', 'LPS3', 'NDPK8', 'PUNP3', 'DMATTx', 'CYSTS', 'CAATPS', 'LEUt4', 'DHFR', 'GLCAASE8ly', 'FAS140COA', 'PETHCT', 'ASPTAm', 'GASNASEly', 'SUCOAS1m', 'RTOTALCRNCPT2', 'PRASCSi', 'ACS', 'TRPt4', 'HEX7', 'FAOXC2031836m', 'ETHAK', 'UAGDP', 'GGH_6THFl', 'SPODMm', 'PDHm', 'GCALDD', 'ABUTD', 'GMPS2', 'PUNP1', 'ACCOAC', 'PTDCACRNt', 'ECOAH1m', '3SALAASPm', 'NACHEX27ly', 'TMNDNCCRNt', 'TTDCRNt', 'RNDR3', 'PRPPS', 'PIK4', 'TYRTA', 'GGH_7THFl', 'PPPGOm', 'EICOSTETCPT1', 'SULFOX', 'DPGM', 'MI3PP', 'FPGS4', 'DGAT', 'AMANK', 'ACGAMK', 'MI4PP', 'FAOXC18280m', 'ACNAM9PL2', 'AGPAT1', 'TMNDNCCPT2', 'MGCHrm', 'FAOXC170m', 'FAOXC18480m', 'DHCR71r', 'NTD9', 'LNSTLSr', 'GK1', 'ACONT', 'PDE1', 'ECOAH12m', 'NDPK7', 'BUTt2r', 'DCSPTN1CPT1', 'THMt3', 'FPGS5m', 'GGH_10FTHF7GLUe', 'GLCURtly', 'DPCOAK', 'FACOAL161', 'TMDS', 'GLBRAN', 'LYSt5r', 'C181CPT1', 'FACOAL260', 'FACOAL245_1', 'GASNASE2ly', 'PIK3', 'C161CRN2t', 'FAOXC1811603m', '3SALATAim', 'NTD6', 'PGCD', 'GALASE1ly', 'CERT2rt', 'FPGS6m', 'FACOAL1821', 'PEAMNO', 'ME2', 'PROt4', 'VACCCPT2', 'GAMt1r', 'PAFH', 'SALMCOM2', 'GBA', 'AIRCr', 'ACGAM6PS', 'AICART', 'STRDNCCPT2', 'ALDD2x', 'C204CPT1', 'FACOAL181', 'FACOAL241', 'FBP26', 'ACRNtm', 'LNELDCCPT2', 'C180CRNt', 'NDPK1', 'C4STMO2Pr', 'C204CPT2', 'FAOXC16180m', 'LNLNCGCRNt', 'GLPASE1', 'MI1PP', 'HEX4', 'FAOXC182806m', 'C161CPT12', 'SBPP1er', 'UREAt', 'RBFK', 'IPDDIx', 'DPMVDx', 'TMNDNCCPT1', 'SLDx', 'RTOTAL3CRNt', 'PI4P5K', 'UDPDOLPT_U', 'LNLCCPT2', 'FTHFLi', 'LNELDCCRNt', 'GGH_5DHFl', 'OCOAT1m', 'LNLNCACPT2', 'HMGCOARx', 'FPGS4m', 'ILEt4', 'PSSA2_hs', 'ACS2', 'FACOAL180', 'UPP3S', 'CHOLK', 'ADRNCRNt', 'PYDXDH', 'CYSTA', 'PUNP7', 'DESAT18_3', 'CTPS1', 'FPGS2', 'LNLCCPT1', 'NTD4e', 'FACOAL150', 'DESAT18_5', 'FAOXC80', 'CDIPTr', 'C160CPT1', 'DHCR243r', 'ARGSL', 'FAOXC204', '24_25VITD3Hm', 'PI45PLC', 'MI14PP', 'FALDH', 'NDPK2', 'AMPTASECG', 'FAS100COA', 'GGH_10FTHF5GLUe', 'DLNLCGCRNt', 'EBP2r', 'C160CPT2', 'EBP1r', 'ADSL1r', 'FACOAL204_copy2', 'NTD11', 'SUCD1m', 'GGH_6THFe', 'PPCDC', 'SOAT11', 'ADMDC', 'OIVD1m', 'VALt4', 'CERK', 'ALDD2xm', 'ALDD2y', 'FACOAL244_1', 'CERT1rt', 'RTOTAL2CRNCPT2', 'FACOAL80', 'BTNt2i', 'C4STMO2r', 'GUACYC', 'MTHFCm', 'ETF', 'FAOXC2252053m', 'C180CPT2', 'CGMPt', 'ADRNCPT1', 'TALA', 'GTHPm', 'SPODMn', 'MCPST', 'CITtam', 'METt4', 'BAMPPALDOX', 'FAOXC161802m', 'CHSTEROLSULT', 'CYSTGLUex', 'DLNLCGCPT2', 'NMNATn', 'HIBDm', 'SADT', 'C4STMO1r', 'RNDR4', 'TKT2', 'PROSTGE1t3', 'GARFT', 'ALDD19xr', 'FAS180COA', 'FPGS9', 'UPPDC1', 'RTOTAL2CRNt', 'FACOAL140', 'AACOAT', 'NDP7ex', '5MTHFt', 'FAOXC2242046m', 'PI4P3K', 'SPRMS', 'GLPASE2', 'PRAIS', 'NaKt', 'UAG2EMA', 'UDPGD', 'HMGCOAS', '3DSPHR', 'ACCOAL', 'AMPTASECGe', 'RNDR1', 'ADSL2r', 'DCSPTN1CRNt', 'DESAT18_10', 'ARGt4', 'FAOXC140', 'DPGase', 'FAEL184', 'VACCCRNt', 'NNATn', 'DCYTD', 'MTHFC', 'STS2', 'GLUPRT', 'THMTP', 'FPGS3', 'ALCD2x', 'PUNP5', 'HMGLm', 'MMEm', 'CREATt4_2_r', 'PI3PP', 'PROSTGE2t3', 'FAOXC16080m', 'H2CO3D', 'PI345P3Pn', 'HACD9m', 'DHCR72r', 'FACOAL160', 'ADSS', 'ACGAMPM', 'TMDK1', 'NTD3', 'ELAIDCRNt', 'DAGKn_hs', 'HPDCACRNCPT1', 'ADPT', 'STS1', 'GLDBRAN', 'RTOTAL3CRNCPT2', 'DGK1', 'NDP8ex', 'FBA4', 'GGH_7THFe', 'FAEL205', 'GALKr', 'ARGLYSex', 'FAOXC1811601m', 'DOPASULT', 'HPDCACRNCPT2', 'SPMS', 'GGH_10FTHF5GLUl', 'TTDCPT2', 'DESAT20_1', 'LNLNCACRNt', 'PI3P4K', 'FACOAL245_2', 'FPGS', 'PI5P3K', 'ADSK', 'DHCR242r', 'DHCRD2', 'LNLCCRNt', 'RNDR2', 'DESAT18_7', '3SALATAi', 'ADK1m', 'C180CPT1', 'LNLNCACPT1', 'C181CPT2', 'ELAIDCPT2', 'RDH2a', 'ARGt5r'], inactive_NC:['24_25DHVITD3t', '7DHFtm', 'P4501B1r', 'EX_hestratriol_e', 'PCHOLPr_hs', 'EX_caro_e', 'DNDPt7m', 'H2Otn', 'GLCURter', 'L_LACDcm', 'PI3P3Pn', 'THMP', 'EX_25hvitd2_e', 'NICRNTtn', 'EX_gtp_e', 'DGK2m', 'FACOAL40im', 'PEFLIP', 'PI345P5Pn', 'EX_but_e', 'DNDPt53m', '10FTHFtl', 'ARTPLM2m', 'UNK3', 'DNDPt57m', 'VITD3Hm', 'ACGAM2E', 'OBDHc', 'DNDPt20m', '7DHFtl', 'CYOR_u10m', 'CYSO', 'DM_dctp_m', 'LEUTA', 'LNLCt', 'ACP1_FMN', 'BALAVECSEC', 'EX_pnto__R_e', 'HSD3A1r', 'BHBt', 'ARTFR52', 'GULN3D', 'PROSTGE2t', 'NADN', 'EX_nrvnc_e', 'GALtly', 'PPAtr', 'HMGCOAtx', 'TCHOLAt3', 'SARCStex', 'O2tm', 'EX_dad_2_e', 'FTHFDH', 'B_MANNASEly', 'CYANt', 'EX_2mcit_e', 'HESTRATRIOLte', 'PPAP', 'ACACT10m', 'ASNNm', 'DOLK_L', 'DNDPt12m', 'EX_fol_e', 'EX_utp_e', 'EX_mercplaccys_e', 'EX_ttdca_e', 'OCBTm', 'DNDPt56m', 'EX_tetpent3_e', 'PA_HSter', 'AKGDm', 'PMTCOAtx', 'COt', 'TTDCAtr', 'RETFAt2', 'PIK4n', 'EX_gam_e', 'GUR1PP', 'DNADDP', 'DNADtn', 'DNDPt58m', 'EX_10fthf7glu_e', 'OCCOAtm', 'URATEtx', 'ASPCT', 'MEOHtly', 'FADDP', 'DNDPt52m', 'OCTAt', 'LRAT', 'ARTFR56', 'DNDPt43m', 'DM_sprm_c', 'DRPA', 'PHACCOAGLNAC', 'EX_pro__L_e', 'RTOT_3', 'DADNt4', 'EX_hexc_e', 'EX_n2m2nmasn_e', 'NADPtru', 'LPS2', 'HAS2', '10FTHF6GLUtl', 'EX_dhf_e', 'MALSO4tm', 'EX_lnlc_e', '5THFtm', 'EX_ppa_e', 'GLUt7l', 'EX_thymd_e', 'EX_pydx_e', 'MCCCrm', 'S2L2N2M2MASNtly', 'GCHOLAt3', 'ACCOALm', 'TYMSFt', 'FADtru', 'XYLK', 'G6PPer', 'CAROtr', 'PYDXtr', 'DADNK', '24_25DHVITD3tm', 'SPHGNtr', 'UNK2', 'BPNT', 'ACGAMtly', 'ACNAMPH', 'FALDtly', '2DR1PP', 'ENGASEly', 'PPAer', 'EX_xoltri25_e', 'CYSGLTH', 'RETH1e', 'PIter', 'MAOX', 'ETOHMO', 'H2O2tn', 'ARTFR46', 'UPPN', 'EX_octa_e', 'AACTtm', 'ACOAO7p', 'FOLt2', 'GHMT2r', 'DNDPt13m', 'PI34P3Pn', 'HPDCAt', 'MI14P4P', 'SLDt', 'PHEMEtm', 'GULNter', 'DNDPt21m', 'UDPGLCter', 'PPItx', 'HISTAVESSEC', 'HSD3B2r', 'EX_3aib_e', 'EX_xolest_hs_e', 'ETHP', 'XOLESTte', 'CO2tp', 'BILIRUBt2', 'EX_hpdca_e', 'MANtly', 'DM_kdn_c', 'EX_pheacgln_e', 'CHOLATEt3', 'EX_camp_e', 'EX_estrones_e', 'EX_val__L_e', 'ACALDtm', 'EX_tetpent6_e', 'C204CRNt', '3SPYRSPm', 'DNDPt30m', 'NADHtru', 'PTRCOX1', 'TETTET6t', '25HVITD2tin', 'ACOAH', 'RETFAt1', 'EX_35cgmp_e', 'CYTDt5', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'PAIL_HStn', 'ESTRONEtr', 'SPHS1Ptr', '3MOPt2im', '6THFtm', 'ARTCOAL1', 'EX_thf_e', 'MCD', 'ACTNMO', 'GND', 'SARDHm', 'EX_his__L_e', 'DHEASULT', 'GGLUCT', 'DNDPt42m', 'PGPP_hs', 'DM_datp_m', 'DM_dgtp_n', 'PIK3n', 'GLUt6', 'ARTPLM1m', 'ENGASE2ly', 'CYSTSERex', 'GLRASE', 'UDPG1P', 'HGNTOR', 'FORtr', 'THFtl', '6DHFtl', 'DNDPt5m', 'HSD3B3r', 'NADtru', 'PI45P4P', 'ATPasel', '10FTHF7GLUtl', 'THMDt4', 'EX_4nphsf_e', 'PE_HSter', 'ARTFR212', 'EX_pe_hs_e', '3SALAOX', 'ACALDtx', 'O2ter', 'DURAD', 'HIStiDF', 'EX_etoh_e', 'EX_retinol_9_cis_e', 'DRBK', 'EX_cysi__L_e', 'NICRNS', 'FBP', 'PAFS', 'URATEt', 'PPAtm', 'SPHK21c', '4PYRDX', 'DOLGPP_Ler', 'ARTFR203', 'DOLGLCP_Lter', 'NACASPAH', 'GLACter', 'ESTRONESt2', 'EX_mepi_e', 'RNMK', 'EX_ocdca_e', 'URIt5', 'DNDPt18m', 'RTOT_2', 'MCLACCYSR', 'CSNATr', 'CYSTGL', 'PA_HStn', 'EX_tcynt_e', 'PGL', 'EX_orn_e', 'PROSTGE1t', 'DOLGLCP_Uter', 'RTOT2', 'SLCBK1', 'DOLP_Uter', 'THFtm', 'EX_ile__L_e', 'MI1PS', 'EX_urea_e', 'DCSPTN1COAtx', 'ADRNCOAtx', 'GLUVESSEC', 'EX_tettet6_e', 'ARTFR45', 'DKMPPD', 'BTNDe', '24_25DHVITD2tm', 'DSAT', 'GLYATm', 'LRAT1', '2MCITt', 'ILETA', 'GCHOLAt2', 'C3STKR2r', '6DHFtm', 'NORANMT', 'DHFtl', 'PDE4', 'DUMPtn', 'CH25H', 'PItx', 'TDP', '3AIBt', 'EX_ocdcea_e', 'DHORD9', 'EX_10fthf_e', 'UDPGNP', 'PNTOt5', 'MI1P_Dtn', '7THFtm', 'DNDPt51m', 'MMTSADm', 'PPPG9tm', 'DHORTS', 'MEPIVESSte', 'AGDC', 'NADPtxu', 'BHBtm', 'GACMTRc', '6THFtl', 'AACTOOR', 'EX_lnlnca_e', 'EX_leu__L_e', 'DUDPtn', 'GLYtm', 'PPBNGS', 'EX_ptdca_e', 'EX_btn_e', '24_25DHVITD2t', 'CRMPte', 'SPH1Pter', 'NCKt', 'RETH', 'EX_4nph_e', 'EX_2425dhvitd2_e', 'H2CO3D2', 'SPMDOX', '3HBCOAHLm', 'PHYCBOXL', 'XOLTRI25te', 'ASNtm', 'ARTFR54', 'P4507B11r', 'PPAn', 'BDHm', 'FUMSO4tm', 'KDNH', 'UREAtm', 'NADtn', '10FTHF6GLUtm', 'PI45P5Pn', '7THFtl', 'EX_thm_e', 'BTNt3i', 'EX_ala_B_e', 'EX_4pyrdx_e', 'CHOLATEt2', 'GTMLTe', 'HISTAtu', 'FDH', 'CO2ter', 'BCDO', 'PROD2', 'HDD2COAtx', '10FTHF5GLUtl', 'ACOAD8m', 'CEPTC', 'HXANtx', 'O2tn', '3AIBTm', 'GPDDA1', 'DNDPt4m', 'EX_thmtp_e', 'GLYK', 'EX_bilirub_e', 'DNDPt31m', 'VALt5m', 'HAS1', 'ARTPLM3m', 'EX_met__L_e', 'PTDCAt', 'DOLGPP_Uer', 'TETPENT6t', 'NADPHtru', 'EX_dopasf_e', 'EX_oxa_e', 'GUAD', 'ARTFR202', 'OPAH', 'HAtly', 'DNDPt3m', 'PItn', 'PRDXl', 'RETH1', 'DOLICHOL_Lter', 'O2Stn', 'DGTPtn', 'CBPS', 'PI4P3Kn', 'UROLACer', 'TCHOLAt2', 'ARTFR13', 'TRDR', 'EX_2425dhvitd3_e', 'ARTFR42', 'DGSNtm', 'LNLNCAt', 'XANtx', 'GLUCYS', 'EX_co_e', 'EX_4abut_e', 'MERCPLACCYSt', 'EX_cmp_e', 'GABAVESSEC', 'EX_arg__L_e', 'NDP6', 'COAtp', 'TMDPPK', 'H2O2tly', 'DINt', 'ADNK1m', 'EX_crmp_hs_e', 'NDP7er', 'NMNtn', 'CSNATm', 'ETOHtx', 'DHFtm', 'EX_cyan_e', 'SPHINGStr', 'PACCOAL', 'EX_trp__L_e', 'DGULND', 'DNDPt2m', 'XYLTD_D', 'FCLTm', '4MOPt2im', 'ASPNATm', 'UDPG4E', 'EX_7dhf_e', '4NPHte', 'TETPENT3t', 'ACNML', 'DPCOAPP', 'PIPLCn', 'FATP9t', 'ETOHt', 'GUAPRT', '10FTHF7GLUtm', 'EX_creat_e', 'ARTFR205', 'PI34P4Pn', 'SERHL', 'RTOT5', 'RAI2', '3SPYRSP', 'ARTFR57', 'CITRtm', 'HEXCt', 'MGSA2', 'DNDPt6m', 'FRDPtr', 'ARTFR211', 'EX_bhb_e', 'AOBUTDsm', 'ACSm', 'HKt', 'MTRI', 'TCYNTt', 'XOLTRI25tc', 'SARCStm', '13DAMPPOX', 'ARTFR210', 'ARTFR209', 'EX_sl__L_e', 'MCITS', 'PI4P4Pn', 'HESTRATRIOLtr', 'PHEACGLNt', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'MDRPD', 'NADPHtxu', '4NPHSFte', 'EX_biocyt_e', 'DOLP_Lter', 'ADPtx', 'LRAT2', 'PROD2m', 'VBOF', 'PI34P5Kn', 'GLNtm', 'CLOHtex2', '10FTHF5GLUtm', 'ARGtm', 'EX_vitd3_e', '34HPPOR', 'DNDPt19m', 'biomass_mac', 'ADCim', 'GSNt4', 'DNDPt54m', 'KHK2', 'EX_sarcs_e', 'DNDPt32m', 'DNDPt1m', 'ETFQO', 'FE2tm', 'MMSAD1m', 'DOLPH_Ler', 'CEPTE', 'GLNLASEer', 'RETH2e', 'DESAT22_1p', 'AHCYStr', 'FUMSO3tm', 'NACASPtm', '5AOPtm', 'AMETr', 'DOPASFt', 'GLCMter', 'PIt2m', 'ARTCOAL2', 'EX_7thf_e', 'N2M2NMASNtly', '3AIBtm', 'EX_5mthf_e', 'EX_retinol_cis_11_e', 'CYTDt4', 'LEUt5m', 'GLYAMDTRc', 'CHSTEROLt2', 'GULLACter', '2AMACSULT', 'EX_urate_e', 'ATPtn', 'EX_tymsf_e', 'RETI1', 'CYOOm3', 'ARTFR43', 'DM_Asn_X_Ser_Thr_l', 'INOSTO', 'THMTPt']\n", + "Reaction BHBtm is not in Z\n", + "1463\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 129\n", + "Reaction no. 851\n", + "Attempting to remove reaction: 3MOPt2im ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1882390000000669\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['OIVD3m', 'ACOAD10m', 'TRIODTHYt2', 'ECOAH9m', 'HACD9m'], inactive_NC:['ILETA', 'TRIODTHYt', 'ACACT10m', '3MOPt2im']\n", + "Reaction 3MOPt2im is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 128\n", + "Reaction no. 852\n", + "Attempting to remove reaction: CSNATr ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.304576999999881\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['ACRNtm'], inactive_NC:['CSNATr', 'CSNATm']\n", + "Reaction CSNATr is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 127\n", + "Reaction no. 853\n", + "Attempting to remove reaction: 4MOPt2im ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 126\n", + "Reaction no. 854\n", + "Attempting to remove reaction: ASPNATm ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 125\n", + "Reaction no. 855\n", + "Attempting to remove reaction: NDP6 ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 29 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2256700000007186\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 30 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'DGAT', 'DCYTD', 'RNDR4'], inactive_NC:['THMDt4', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'PEFLIP', 'NDP6', 'AHCYStr']\n", + "Reaction NDP6 is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 124\n", + "Reaction no. 856\n", + "Attempting to remove reaction: 3HBCOAHLm ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 12 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.174579000000449\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 13 , inactive_C: ['OIVD2m', 'ACOAD9m', 'HIBDm', 'ECOAH12m', 'VALTAim'], inactive_NC:['MMSAD1m', '3AIBtm', 'MMTSADm', 'EX_3aib_e', 'VALt5m', '3HBCOAHLm', '3AIBTm', '3AIBt']\n", + "Reaction 3HBCOAHLm is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 123\n", + "Reaction no. 857\n", + "Attempting to remove reaction: NDP7er ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 13 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2780249999996158\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 14 , inactive_C: ['UGCG', 'NKCC2t', 'CERT1rt', 'CREATt4_2_r', 'TRIODTHYt2', 'CERT2rt', 'GBA', 'SERtN1'], inactive_NC:['UDPGLCter', 'EX_creat_e', 'GLYAMDTRc', 'NDP7er', 'GACMTRc', 'TRIODTHYt']\n", + "Reaction NDP7er is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 122\n", + "Reaction no. 858\n", + "Attempting to remove reaction: DSAT ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 41 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.534787000000506\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 42 , inactive_C: ['DUTPDPn', 'PETOHMr_hs', 'SMS', 'PGPPT', 'PUNP1', 'DCYTD', 'RNDR4', 'THYMDt1', 'PSSA2_hs', 'TRIODTHYt2', 'CERK', 'DHCRD2', 'FACOAL161', 'TMDS', 'PETHCT', 'DGAT', '3DSPHR', 'NTD3', 'DHCRD1', 'NDPK6n', 'SERPT'], inactive_NC:['EX_pi_e', 'CEPTE', 'PA_HSter', 'EX_crmp_hs_e', 'TRIODTHYt', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'PCHOLPr_hs', 'PGPP_hs', 'DSAT', 'CRMPte', 'DUMPtn', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'NDP6']\n", + "Reaction DSAT is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 121\n", + "Reaction no. 859\n", + "Attempting to remove reaction: 4PYRDX ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1712769999994634\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['PYDXDH'], inactive_NC:['EX_4pyrdx_e', 'EX_pydx_e', 'GLYtm', '4PYRDX', 'PYDXtr']\n", + "Reaction 4PYRDX is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 120\n", + "Reaction no. 860\n", + "Attempting to remove reaction: MEPIVESSte ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3697959999999512\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['SALMCOM2', 'NKCC2t', 'TRIODTHYt2'], inactive_NC:['EX_mepi_e', 'MEPIVESSte', 'TRIODTHYt']\n", + "Reaction MEPIVESSte is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 119\n", + "Reaction no. 861\n", + "Attempting to remove reaction: biomass_mac ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 33 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4755649999997331\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 34 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'TRIODTHYt2', 'SMS', 'PGPPT', 'NDPK6n', 'PUNP1', 'DGAT', 'DCYTD', 'RNDR4'], inactive_NC:['THMDt4', 'biomass_mac', 'PE_HSter', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'CEPTE', 'DUDPtn', 'DUMPtn', 'PA_HSter', 'GLCt4', 'EX_pe_hs_e', 'PCHOLPr_hs', 'PGPP_hs', 'PEFLIP', 'NDP6', 'TRIODTHYt', 'AHCYStr']\n", + "Reaction biomass_mac is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 118\n", + "Reaction no. 862\n", + "Attempting to remove reaction: VBOF ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.16204099999959\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['VBOF', 'TRIODTHYt']\n", + "Reaction VBOF is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 117\n", + "Reaction no. 863\n", + "Attempting to remove reaction: MCITS ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4449309999999969\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['ACS2', 'ACITL', 'CREATt4_2_r', 'SERtN1', 'ACCOAL'], inactive_NC:['2MCITt', 'EX_creat_e', 'GLYAMDTRc', 'OBDHc', 'GACMTRc', 'EX_2mcit_e', 'MCITS']\n", + "Reaction MCITS is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 116\n", + "Reaction no. 864\n", + "Attempting to remove reaction: TRIOK ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4565750000001572\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['TRIODTHYt2', 'FBA2'], inactive_NC:['KHK', 'TRIOK', 'TRIODTHYt']\n", + "Reaction TRIOK is not in Z\n", + "1463\n", + "1463\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 115\n", + "Reaction no. 865\n", + "Attempting to remove reaction: MMTSADm ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.136569999999665\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['MMTSADm', 'TRIODTHYt']\n", + "Reaction MMTSADm is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 114\n", + "Reaction no. 866\n", + "Attempting to remove reaction: HISTAtu ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0830940000005285\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['PUNP1', 'TRIODTHYt2'], inactive_NC:['HISTAVESSEC', 'HISTAtu', 'TRIODTHYt']\n", + "Reaction HISTAtu is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 113\n", + "Reaction no. 867\n", + "Attempting to remove reaction: MALTt1r ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.415646000000379\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['MALT', 'PUNP1', 'TRIODTHYt2'], inactive_NC:['MALTt1r', 'TRIODTHYt']\n", + "Reaction MALTt1r is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 112\n", + "Reaction no. 868\n", + "Attempting to remove reaction: MALSO4tm ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 111\n", + "Reaction no. 869\n", + "Attempting to remove reaction: FUMSO3tm ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0995160000002215\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['3SALATAim', '3SALAASPm'], inactive_NC:['FUMSO3tm', '3SPYRSPm']\n", + "Reaction FUMSO3tm is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 110\n", + "Reaction no. 870\n", + "Attempting to remove reaction: FUMSO4tm ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 109\n", + "Reaction no. 871\n", + "Attempting to remove reaction: FE3R2e ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 11 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1434010000002672\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 12 , inactive_C: ['CREATt4_2_r', 'NKCC2t', 'DHAAt1r', 'TRIODTHYt2'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'EX_fe2_e', 'EX_fe3_e', 'FE3R2e', 'ASCBt4', 'GACMTRc', 'TRIODTHYt']\n", + "Reaction FE3R2e is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 108\n", + "Reaction no. 872\n", + "Attempting to remove reaction: 13DAMPPOX ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.42252500000086\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['CREATt4_2_r', 'BAMPPALDOX'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', '13DAMPPOX', 'SPMDOX', 'GLCt4', 'GACMTRc']\n", + "Reaction 13DAMPPOX is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 107\n", + "Reaction no. 873\n", + "Attempting to remove reaction: MAOX ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4359130000002551\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['41R1H2MAE12BOOX', 'TRIODTHYt2', 'SFGTHi', 'PUNP1', 'FALDH'], inactive_NC:['EX_pi_e', 'MAOX', 'TRIODTHYt']\n", + "Reaction MAOX is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 106\n", + "Reaction no. 874\n", + "Attempting to remove reaction: PTRCOX1 ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0876170000001366\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['PUNP1'], inactive_NC:['NH4t3r', 'PTRCOX1']\n", + "Reaction PTRCOX1 is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 105\n", + "Reaction no. 875\n", + "Attempting to remove reaction: FCLTm ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 104\n", + "Reaction no. 876\n", + "Attempting to remove reaction: TCHOLAt2 ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4412290000000212\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GLUt2m', 'TRIODTHYt2'], inactive_NC:['TCHOLAt2', 'TCHOLAt3', 'TRIODTHYt']\n", + "Reaction TCHOLAt2 is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 963 (119 core, 844 non-core); Num. remaining: 103\n", + "Reaction no. 877\n", + "Attempting to remove reaction: GCHOLAt2 ...\n", + "Initial PM reactions: 1463\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.391233000000284\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['GCHOLAt3', 'GCHOLAt2']\n", + "Reaction GCHOLAt2 is not in Z\n", + "1463\n", + "1463\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1461\n", + "Num. removed: 965 (119 core, 846 non-core); Num. remaining: 101\n", + "Reaction no. 878\n", + "Attempting to remove reaction: CHOLATEt2 ...\n", + "Initial PM reactions: 1461\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1508589999994001\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['GDHm'], inactive_NC:['CHOLATEt2', 'CHOLATEt3']\n", + "Reaction CHOLATEt2 is not in Z\n", + "1461\n", + "1461\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 965 (119 core, 846 non-core); Num. remaining: 100\n", + "Reaction no. 879\n", + "Attempting to remove reaction: P4507B11r ...\n", + "Initial PM reactions: 1461\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.422219000000041\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: [], inactive_NC:['XOLTRI25te', 'P4507B11r', 'EX_xoltri25_e', 'XOLTRI25tc', 'CH25H']\n", + "Reaction P4507B11r is not in Z\n", + "1461\n", + "1461\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1456\n", + "Num. removed: 970 (119 core, 851 non-core); Num. remaining: 98\n", + "Reaction no. 880\n", + "Attempting to remove reaction: CYSTGL ...\n", + "Initial PM reactions: 1456\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4091699999999037\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['CYSTS', '2HBt2', '2HBO', 'TRIODTHYt2'], inactive_NC:['CYSTGL', 'TRIODTHYt', 'EX_2hb_e']\n", + "Reaction CYSTGL is not in Z\n", + "1456\n", + "1456\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 970 (119 core, 851 non-core); Num. remaining: 97\n", + "Reaction no. 881\n", + "Attempting to remove reaction: TRIODTHYt ...\n", + "Initial PM reactions: 1456\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.107970000000023\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['HCO3_CLt', 'TRIODTHYt2'], inactive_NC:['TRIODTHYt']\n", + "Reaction TRIODTHYt is not in Z\n", + "1456\n", + "1456\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 970 (119 core, 851 non-core); Num. remaining: 96\n", + "Reaction no. 882\n", + "Attempting to remove reaction: H2O2syn ...\n", + "Initial PM reactions: 1456\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3949060000004465\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['H2O2syn', 'TRIODTHYt']\n", + "Reaction H2O2syn is not in Z\n", + "1456\n", + "1456\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 970 (119 core, 851 non-core); Num. remaining: 95\n", + "Reaction no. 883\n", + "Attempting to remove reaction: DOPABMO ...\n", + "Initial PM reactions: 1456\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 12 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.479707999999846\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 13 , inactive_C: ['34DHOXPEGOX', '41R1H2MAE12BOOX', 'SALMCOM2', 'SFGTHi', '41R2A1H12BOOX', 'FALDH'], inactive_NC:['DOPABMO', 'EX_34dhoxpeg_e', 'NORANMT', '34DHOXPEGt', 'MEPIVESSte', 'MAOX', 'EX_mepi_e']\n", + "Reaction DOPABMO is not in Z\n", + "1456\n", + "1456\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 970 (119 core, 851 non-core); Num. remaining: 94\n", + "Reaction no. 884\n", + "Attempting to remove reaction: BTNDe ...\n", + "Initial PM reactions: 1456\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 41 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2918190000000322\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 42 , inactive_C: ['THYMDt1', 'DUTPDPn', 'FACOAL161', 'PSSA2_hs', 'NTD3', 'PROt4', 'TMDS', 'PETHCT', 'PETOHMr_hs', 'SMS', 'PGPPT', 'NDPK6n', 'PUNP1', 'DGAT', 'HISt4', 'DCYTD', 'RNDR4', 'TRPt4'], inactive_NC:['CEPTE', 'PA_HSter', 'EX_his__L_e', 'AHCYStr', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'EX_trp__L_e', 'PCHOLPr_hs', 'BTNDe', 'EX_btn_e', 'PGPP_hs', 'EX_biocyt_e', 'DUMPtn', 'VBOF', 'PEFLIP', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'EX_pro__L_e', 'NDP6', 'HIStiDF']\n", + "Reaction BTNDe is not in Z\n", + "1456\n", + "1456\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 970 (119 core, 851 non-core); Num. remaining: 93\n", + "Reaction no. 885\n", + "Attempting to remove reaction: PGL ...\n", + "Initial PM reactions: 1456\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4854459999996834\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['G6PDH2r', 'RPI', 'TRIODTHYt2'], inactive_NC:['PGL', 'GND', 'TRIODTHYt']\n", + "Reaction PGL is not in Z\n", + "1456\n", + "1456\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 970 (119 core, 851 non-core); Num. remaining: 92\n", + "Reaction no. 886\n", + "Attempting to remove reaction: PPBNGS ...\n", + "Initial PM reactions: 1456\n", + "check_model_function done ....\n", + "Num. removed: 970 (119 core, 851 non-core); Num. remaining: 91\n", + "Reaction no. 887\n", + "Attempting to remove reaction: ACTNMO ...\n", + "Initial PM reactions: 1456\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1606059999994613\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['LEUTAm', 'ACETONEt2m'], inactive_NC:['ADCim', 'ACTNMO', 'LEUt5m']\n", + "Reaction ACTNMO is not in Z\n", + "1456\n", + "1456\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 970 (119 core, 851 non-core); Num. remaining: 90\n", + "Reaction no. 888\n", + "Attempting to remove reaction: ETOHMO ...\n", + "Initial PM reactions: 1456\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1307870000000548\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['ETOHMO', 'TRIODTHYt']\n", + "Reaction ETOHMO is not in Z\n", + "1456\n", + "1456\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 970 (119 core, 851 non-core); Num. remaining: 89\n", + "Reaction no. 889\n", + "Attempting to remove reaction: GLYK ...\n", + "Initial PM reactions: 1456\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 10 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3597869999994145\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 11 , inactive_C: ['GLCt1', 'CREATt4_2_r', 'LPS3', 'TRIODTHYt2'], inactive_NC:['EX_pi_e', 'EX_creat_e', 'GLYAMDTRc', 'LPS2', 'GLYK', 'GACMTRc', 'TRIODTHYt']\n", + "Reaction GLYK is not in Z\n", + "1456\n", + "1456\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 970 (119 core, 851 non-core); Num. remaining: 88\n", + "Reaction no. 890\n", + "Attempting to remove reaction: ACTLMO ...\n", + "Initial PM reactions: 1456\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3791929999997592\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['ACTLMO']\n", + "Reaction ACTLMO is not in Z\n", + "1456\n", + "1456\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1455\n", + "Num. removed: 971 (119 core, 852 non-core); Num. remaining: 87\n", + "Reaction no. 891\n", + "Attempting to remove reaction: Htm ...\n", + "Initial PM reactions: 1455\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0250120000000607\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['Htm']\n", + "Reaction Htm is not in Z\n", + "1455\n", + "1455\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1454\n", + "Num. removed: 972 (119 core, 853 non-core); Num. remaining: 86\n", + "Reaction no. 892\n", + "Attempting to remove reaction: TCHOLAt3 ...\n", + "Initial PM reactions: 1454\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4022279999999228\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['TCHOLAt2', 'TCHOLAt3']\n", + "Reaction TCHOLAt3 is not in Z\n", + "1454\n", + "1454\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1452\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 85\n", + "Reaction no. 893\n", + "Attempting to remove reaction: CHOLATEt3 ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3897950000000492\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['SERtN1', 'CREATt4_2_r', 'NKCC2t', 'TRIODTHYt2'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'CHOLATEt2', 'CHOLATEt3', 'GACMTRc', 'TRIODTHYt']\n", + "Reaction CHOLATEt3 is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 84\n", + "Reaction no. 894\n", + "Attempting to remove reaction: CLI2tex ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0966129999997065\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['CREATt4_2_r', 'NAIt', 'GDHm'], inactive_NC:['GACMTRc', 'EX_creat_e', 'CLI2tex', 'GLYAMDTRc']\n", + "Reaction CLI2tex is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 83\n", + "Reaction no. 895\n", + "Attempting to remove reaction: FDH ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4062670000002981\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['PUNP1'], inactive_NC:['FDH']\n", + "Reaction FDH is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 82\n", + "Reaction no. 896\n", + "Attempting to remove reaction: PROSTGE2t ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0878350000002683\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['PROSTGE2t3', 'GLUt2m', 'LEUTAm'], inactive_NC:['LEUt5m', 'PROSTGE2t']\n", + "Reaction PROSTGE2t is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 81\n", + "Reaction no. 897\n", + "Attempting to remove reaction: DNDPt51m ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0781710000001112\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['CREATt4_2_r'], inactive_NC:['DNDPt51m', 'GACMTRc', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction DNDPt51m is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 80\n", + "Reaction no. 898\n", + "Attempting to remove reaction: DNDPt7m ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.265190000000075\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['GLUt2m', '2HBt2', '2HBO', 'TRIODTHYt2'], inactive_NC:['DNDPt7m', 'TRIODTHYt', 'EX_2hb_e']\n", + "Reaction DNDPt7m is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 79\n", + "Reaction no. 899\n", + "Attempting to remove reaction: DNDPt3m ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3366550000000643\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GLUt2m'], inactive_NC:['DNDPt3m']\n", + "Reaction DNDPt3m is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 78\n", + "Reaction no. 900\n", + "Attempting to remove reaction: DNDPt62m ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1054219999996349\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['LEUTAm'], inactive_NC:['LEUt5m', 'DNDPt62m']\n", + "Reaction DNDPt62m is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 77\n", + "Reaction no. 901\n", + "Attempting to remove reaction: DNDPt54m ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3578310000002602\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GLUt2m', 'LEUTAm'], inactive_NC:['DNDPt54m', 'LEUt5m', 'GLCt4']\n", + "Reaction DNDPt54m is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 76\n", + "Reaction no. 902\n", + "Attempting to remove reaction: DNDPt63m ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3869379999996454\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['LEUTAm'], inactive_NC:['DNDPt63m', 'LEUt5m']\n", + "Reaction DNDPt63m is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 75\n", + "Reaction no. 903\n", + "Attempting to remove reaction: DNDPt52m ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1838619999998627\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GLUt2m', 'MTHFD2m', 'LEUTAm'], inactive_NC:['LEUt5m', 'DNDPt52m']\n", + "Reaction DNDPt52m is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 74\n", + "Reaction no. 904\n", + "Attempting to remove reaction: DNDPt53m ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3775040000000445\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GLUt2m', 'MTHFD2m', 'LEUTAm'], inactive_NC:['LEUt5m', 'DNDPt53m']\n", + "Reaction DNDPt53m is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 974 (119 core, 855 non-core); Num. remaining: 73\n", + "Reaction no. 905\n", + "Attempting to remove reaction: DNDPt5m ...\n", + "Initial PM reactions: 1452\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.304016000000047\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['DNDPt5m']\n", + "Reaction DNDPt5m is not in Z\n", + "1452\n", + "1452\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1451\n", + "Num. removed: 975 (119 core, 856 non-core); Num. remaining: 72\n", + "Reaction no. 906\n", + "Attempting to remove reaction: DNDPt38m ...\n", + "Initial PM reactions: 1451\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.128686999999445\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['LEUTAm'], inactive_NC:['LEUt5m', 'DNDPt38m']\n", + "Reaction DNDPt38m is not in Z\n", + "1451\n", + "1451\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 975 (119 core, 856 non-core); Num. remaining: 71\n", + "Reaction no. 907\n", + "Attempting to remove reaction: DNDPt61m ...\n", + "Initial PM reactions: 1451\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1708010000002105\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GLUt2m'], inactive_NC:['DNDPt61m']\n", + "Reaction DNDPt61m is not in Z\n", + "1451\n", + "1451\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 975 (119 core, 856 non-core); Num. remaining: 70\n", + "Reaction no. 908\n", + "Attempting to remove reaction: DNDPt41m ...\n", + "Initial PM reactions: 1451\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3910219999997935\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['DNDPt41m']\n", + "Reaction DNDPt41m is not in Z\n", + "1451\n", + "1451\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1450\n", + "Num. removed: 976 (119 core, 857 non-core); Num. remaining: 69\n", + "Reaction no. 909\n", + "Attempting to remove reaction: DNDPt59m ...\n", + "Initial PM reactions: 1450\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3974320000006628\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['DNDPt59m', 'TRIODTHYt']\n", + "Reaction DNDPt59m is not in Z\n", + "1450\n", + "1450\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 976 (119 core, 857 non-core); Num. remaining: 68\n", + "Reaction no. 910\n", + "Attempting to remove reaction: DNDPt4m ...\n", + "Initial PM reactions: 1450\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.09259800000018\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['DNDPt4m', 'TRIODTHYt']\n", + "Reaction DNDPt4m is not in Z\n", + "1450\n", + "1450\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 976 (119 core, 857 non-core); Num. remaining: 67\n", + "Reaction no. 911\n", + "Attempting to remove reaction: DNDPt6m ...\n", + "Initial PM reactions: 1450\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.094782000000123\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['TRIODTHYt2', 'GDHm'], inactive_NC:['DNDPt6m', 'TRIODTHYt']\n", + "Reaction DNDPt6m is not in Z\n", + "1450\n", + "1450\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 976 (119 core, 857 non-core); Num. remaining: 66\n", + "Reaction no. 912\n", + "Attempting to remove reaction: DNDPt37m ...\n", + "Initial PM reactions: 1450\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3951109999998152\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['NKCC2t', 'TRIODTHYt2'], inactive_NC:['DNDPt37m', 'TRIODTHYt']\n", + "Reaction DNDPt37m is not in Z\n", + "1450\n", + "1450\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 976 (119 core, 857 non-core); Num. remaining: 65\n", + "Reaction no. 913\n", + "Attempting to remove reaction: DNDPt60m ...\n", + "Initial PM reactions: 1450\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3817310000004\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['HCO3_CLt'], inactive_NC:['DNDPt60m']\n", + "Reaction DNDPt60m is not in Z\n", + "1450\n", + "1450\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 976 (119 core, 857 non-core); Num. remaining: 64\n", + "Reaction no. 914\n", + "Attempting to remove reaction: DNDPt40m ...\n", + "Initial PM reactions: 1450\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.132090000000062\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['DNDPt40m', 'TRIODTHYt']\n", + "Reaction DNDPt40m is not in Z\n", + "1450\n", + "1450\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 976 (119 core, 857 non-core); Num. remaining: 63\n", + "Reaction no. 915\n", + "Attempting to remove reaction: DNDPt39m ...\n", + "Initial PM reactions: 1450\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3867249999993874\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GDHm'], inactive_NC:['DNDPt39m']\n", + "Reaction DNDPt39m is not in Z\n", + "1450\n", + "1450\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 976 (119 core, 857 non-core); Num. remaining: 62\n", + "Reaction no. 916\n", + "Attempting to remove reaction: DNDPt25m ...\n", + "Initial PM reactions: 1450\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1385110000001077\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['EX_pi_e', 'DNDPt25m']\n", + "Reaction DNDPt25m is not in Z\n", + "1450\n", + "1450\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 976 (119 core, 857 non-core); Num. remaining: 61\n", + "Reaction no. 917\n", + "Attempting to remove reaction: DNDPt27m ...\n", + "Initial PM reactions: 1450\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1046479999995427\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['DNDPt27m']\n", + "Reaction DNDPt27m is not in Z\n", + "1450\n", + "1450\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1449\n", + "Num. removed: 977 (119 core, 858 non-core); Num. remaining: 60\n", + "Reaction no. 918\n", + "Attempting to remove reaction: DNDPt10m ...\n", + "Initial PM reactions: 1449\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3270659999998315\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['NKCC2t', 'TRIODTHYt2'], inactive_NC:['DNDPt10m', 'TRIODTHYt']\n", + "Reaction DNDPt10m is not in Z\n", + "1449\n", + "1449\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 977 (119 core, 858 non-core); Num. remaining: 59\n", + "Reaction no. 919\n", + "Attempting to remove reaction: DNDPt29m ...\n", + "Initial PM reactions: 1449\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3360599999996339\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['DNDPt29m']\n", + "Reaction DNDPt29m is not in Z\n", + "1449\n", + "1449\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1448\n", + "Num. removed: 978 (119 core, 859 non-core); Num. remaining: 58\n", + "Reaction no. 920\n", + "Attempting to remove reaction: DNDPt17m ...\n", + "Initial PM reactions: 1448\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.085268000000724\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GDHm'], inactive_NC:['DNDPt17m']\n", + "Reaction DNDPt17m is not in Z\n", + "1448\n", + "1448\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 978 (119 core, 859 non-core); Num. remaining: 57\n", + "Reaction no. 921\n", + "Attempting to remove reaction: DNDPt26m ...\n", + "Initial PM reactions: 1448\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3939679999994041\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['DNDPt26m', 'TRIODTHYt']\n", + "Reaction DNDPt26m is not in Z\n", + "1448\n", + "1448\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 978 (119 core, 859 non-core); Num. remaining: 56\n", + "Reaction no. 922\n", + "Attempting to remove reaction: DNDPt28m ...\n", + "Initial PM reactions: 1448\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4276979999995092\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['HCO3_CLt'], inactive_NC:['DNDPt28m']\n", + "Reaction DNDPt28m is not in Z\n", + "1448\n", + "1448\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 978 (119 core, 859 non-core); Num. remaining: 55\n", + "Reaction no. 923\n", + "Attempting to remove reaction: DNDPt36m ...\n", + "Initial PM reactions: 1448\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1579910000000382\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['PUNP1', 'TRIODTHYt2'], inactive_NC:['DNDPt36m', 'TRIODTHYt']\n", + "Reaction DNDPt36m is not in Z\n", + "1448\n", + "1448\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 978 (119 core, 859 non-core); Num. remaining: 54\n", + "Reaction no. 924\n", + "Attempting to remove reaction: DNDPt24m ...\n", + "Initial PM reactions: 1448\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.036446999999498\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['DNDPt24m']\n", + "Reaction DNDPt24m is not in Z\n", + "1448\n", + "1448\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1447\n", + "Num. removed: 979 (119 core, 860 non-core); Num. remaining: 53\n", + "Reaction no. 925\n", + "Attempting to remove reaction: DNDPt9m ...\n", + "Initial PM reactions: 1447\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 8 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3896409999997559\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 9 , inactive_C: ['CREATt4_2_r', 'NKCC2t', 'MTHFD2m', 'TRIODTHYt2'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'DNDPt9m', 'GACMTRc', 'TRIODTHYt']\n", + "Reaction DNDPt9m is not in Z\n", + "1447\n", + "1447\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 979 (119 core, 860 non-core); Num. remaining: 52\n", + "Reaction no. 926\n", + "Attempting to remove reaction: DNDPt14m ...\n", + "Initial PM reactions: 1447\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4193760000007387\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['CREATt4_2_r', 'SERtN1', 'TRIODTHYt2'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'DNDPt14m', 'GACMTRc', 'TRIODTHYt']\n", + "Reaction DNDPt14m is not in Z\n", + "1447\n", + "1447\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 979 (119 core, 860 non-core); Num. remaining: 51\n", + "Reaction no. 927\n", + "Attempting to remove reaction: DNDPt22m ...\n", + "Initial PM reactions: 1447\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.114169999999831\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['HCO3_CLt'], inactive_NC:['DNDPt22m', 'EX_pi_e']\n", + "Reaction DNDPt22m is not in Z\n", + "1447\n", + "1447\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 979 (119 core, 860 non-core); Num. remaining: 50\n", + "Reaction no. 928\n", + "Attempting to remove reaction: DNDPt23m ...\n", + "Initial PM reactions: 1447\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3998750000000655\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['TRIODTHYt2'], inactive_NC:['DNDPt23m', 'EX_pi_e', 'NH4t3r', 'TRIODTHYt']\n", + "Reaction DNDPt23m is not in Z\n", + "1447\n", + "1447\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 979 (119 core, 860 non-core); Num. remaining: 49\n", + "Reaction no. 929\n", + "Attempting to remove reaction: DNDPt34m ...\n", + "Initial PM reactions: 1447\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3762010000000373\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: [], inactive_NC:['EX_pi_e', 'DNDPt34m']\n", + "Reaction DNDPt34m is not in Z\n", + "1447\n", + "1447\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 979 (119 core, 860 non-core); Num. remaining: 48\n", + "Reaction no. 930\n", + "Attempting to remove reaction: DNDPt8m ...\n", + "Initial PM reactions: 1447\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1871639999999388\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GLUt2m'], inactive_NC:['DNDPt8m']\n", + "Reaction DNDPt8m is not in Z\n", + "1447\n", + "1447\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 979 (119 core, 860 non-core); Num. remaining: 47\n", + "Reaction no. 931\n", + "Attempting to remove reaction: DNDPt16m ...\n", + "Initial PM reactions: 1447\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0846879999999146\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['GDHm', 'TRIODTHYt2'], inactive_NC:['DNDPt16m', 'TRIODTHYt']\n", + "Reaction DNDPt16m is not in Z\n", + "1447\n", + "1447\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 979 (119 core, 860 non-core); Num. remaining: 46\n", + "Reaction no. 932\n", + "Attempting to remove reaction: DNDPt11m ...\n", + "Initial PM reactions: 1447\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3532810000006066\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['DNDPt11m']\n", + "Reaction DNDPt11m is not in Z\n", + "1447\n", + "1447\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1446\n", + "Num. removed: 980 (119 core, 861 non-core); Num. remaining: 45\n", + "Reaction no. 933\n", + "Attempting to remove reaction: DNDPt35m ...\n", + "Initial PM reactions: 1446\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0861580000000686\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['LEUTAm'], inactive_NC:['DNDPt35m', 'LEUt5m']\n", + "Reaction DNDPt35m is not in Z\n", + "1446\n", + "1446\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 980 (119 core, 861 non-core); Num. remaining: 44\n", + "Reaction no. 934\n", + "Attempting to remove reaction: DNDPt33m ...\n", + "Initial PM reactions: 1446\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.165516000000025\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['LEUTAm'], inactive_NC:['DNDPt33m', 'LEUt5m']\n", + "Reaction DNDPt33m is not in Z\n", + "1446\n", + "1446\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 980 (119 core, 861 non-core); Num. remaining: 43\n", + "Reaction no. 935\n", + "Attempting to remove reaction: DNDPt15m ...\n", + "Initial PM reactions: 1446\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4567250000000058\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['CREATt4_2_r'], inactive_NC:['GACMTRc', 'GLYAMDTRc', 'EX_creat_e', 'DNDPt15m']\n", + "Reaction DNDPt15m is not in Z\n", + "1446\n", + "1446\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 980 (119 core, 861 non-core); Num. remaining: 42\n", + "Reaction no. 936\n", + "Attempting to remove reaction: NCKt ...\n", + "Initial PM reactions: 1446\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3571770000007746\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['CAATPS', 'PUNP1'], inactive_NC:['EX_pi_e', 'NCKt']\n", + "Reaction NCKt is not in Z\n", + "1446\n", + "1446\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 980 (119 core, 861 non-core); Num. remaining: 41\n", + "Reaction no. 937\n", + "Attempting to remove reaction: DNDPt55m ...\n", + "Initial PM reactions: 1446\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.229537999999593\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['CREATt4_2_r'], inactive_NC:['DNDPt55m', 'GACMTRc', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction DNDPt55m is not in Z\n", + "1446\n", + "1446\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 980 (119 core, 861 non-core); Num. remaining: 40\n", + "Reaction no. 938\n", + "Attempting to remove reaction: DNDPt1m ...\n", + "Initial PM reactions: 1446\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.021864999999707\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['DNDPt1m']\n", + "Reaction DNDPt1m is not in Z\n", + "1446\n", + "1446\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1445\n", + "Num. removed: 981 (119 core, 862 non-core); Num. remaining: 39\n", + "Reaction no. 939\n", + "Attempting to remove reaction: DNDPt58m ...\n", + "Initial PM reactions: 1445\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.330601999999999\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['DNDPt58m']\n", + "Reaction DNDPt58m is not in Z\n", + "1445\n", + "1445\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1444\n", + "Num. removed: 982 (119 core, 863 non-core); Num. remaining: 38\n", + "Reaction no. 940\n", + "Attempting to remove reaction: DNDPt42m ...\n", + "Initial PM reactions: 1444\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.319985000000088\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GLCt1'], inactive_NC:['DNDPt42m']\n", + "Reaction DNDPt42m is not in Z\n", + "1444\n", + "1444\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 982 (119 core, 863 non-core); Num. remaining: 37\n", + "Reaction no. 941\n", + "Attempting to remove reaction: PGK ...\n", + "Initial PM reactions: 1444\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.04691400000047\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['PGK']\n", + "Reaction PGK is not in Z\n", + "1444\n", + "1444\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1443\n", + "Num. removed: 983 (119 core, 864 non-core); Num. remaining: 36\n", + "Reaction no. 942\n", + "Attempting to remove reaction: DNDPt30m ...\n", + "Initial PM reactions: 1443\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4107869999998002\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['TRIODTHYt', 'DNDPt30m']\n", + "Reaction DNDPt30m is not in Z\n", + "1443\n", + "1443\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 983 (119 core, 864 non-core); Num. remaining: 35\n", + "Reaction no. 943\n", + "Attempting to remove reaction: DNDPt12m ...\n", + "Initial PM reactions: 1443\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3734679999997752\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['2HBt2', '2HBO'], inactive_NC:['DNDPt12m', 'EX_2hb_e']\n", + "Reaction DNDPt12m is not in Z\n", + "1443\n", + "1443\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 983 (119 core, 864 non-core); Num. remaining: 34\n", + "Reaction no. 944\n", + "Attempting to remove reaction: DNDPt21m ...\n", + "Initial PM reactions: 1443\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1143529999999373\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['TRIODTHYt2', 'NKCC2t', 'GDHm'], inactive_NC:['DNDPt21m', 'TRIODTHYt']\n", + "Reaction DNDPt21m is not in Z\n", + "1443\n", + "1443\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 983 (119 core, 864 non-core); Num. remaining: 33\n", + "Reaction no. 945\n", + "Attempting to remove reaction: DNDPt18m ...\n", + "Initial PM reactions: 1443\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3767010000001392\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['DNDPt18m', 'TRIODTHYt']\n", + "Reaction DNDPt18m is not in Z\n", + "1443\n", + "1443\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 983 (119 core, 864 non-core); Num. remaining: 32\n", + "Reaction no. 946\n", + "Attempting to remove reaction: DNDPt56m ...\n", + "Initial PM reactions: 1443\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3756549999998242\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['TRIODTHYt2'], inactive_NC:['TRIODTHYt', 'DNDPt56m']\n", + "Reaction DNDPt56m is not in Z\n", + "1443\n", + "1443\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 983 (119 core, 864 non-core); Num. remaining: 31\n", + "Reaction no. 947\n", + "Attempting to remove reaction: DNDPt2m ...\n", + "Initial PM reactions: 1443\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0570459999999002\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['DNDPt2m']\n", + "Reaction DNDPt2m is not in Z\n", + "1443\n", + "1443\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1442\n", + "Num. removed: 984 (119 core, 865 non-core); Num. remaining: 30\n", + "Reaction no. 948\n", + "Attempting to remove reaction: DNDPt57m ...\n", + "Initial PM reactions: 1442\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4073800000005576\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['ENO', 'NKCC2t', 'TRIODTHYt2', 'PGM'], inactive_NC:['EX_pi_e', 'DNDPt57m', 'TRIODTHYt']\n", + "Reaction DNDPt57m is not in Z\n", + "1442\n", + "1442\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 984 (119 core, 865 non-core); Num. remaining: 29\n", + "Reaction no. 949\n", + "Attempting to remove reaction: DNDPt43m ...\n", + "Initial PM reactions: 1442\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3257489999996324\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['PUNP1'], inactive_NC:['DNDPt43m']\n", + "Reaction DNDPt43m is not in Z\n", + "1442\n", + "1442\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 984 (119 core, 865 non-core); Num. remaining: 28\n", + "Reaction no. 950\n", + "Attempting to remove reaction: RNMK ...\n", + "Initial PM reactions: 1442\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1786669999992228\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['NMNATn', 'PNP', 'ADPRDP'], inactive_NC:['RNMK', 'NADtn', 'NADN', 'NMNtn']\n", + "Reaction RNMK is not in Z\n", + "1442\n", + "1442\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 984 (119 core, 865 non-core); Num. remaining: 27\n", + "Reaction no. 951\n", + "Attempting to remove reaction: DNDPt31m ...\n", + "Initial PM reactions: 1442\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4086409999999887\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['PUNP1', 'TRIODTHYt2'], inactive_NC:['DNDPt31m', 'TRIODTHYt']\n", + "Reaction DNDPt31m is not in Z\n", + "1442\n", + "1442\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 984 (119 core, 865 non-core); Num. remaining: 26\n", + "Reaction no. 952\n", + "Attempting to remove reaction: FTHFDH ...\n", + "Initial PM reactions: 1442\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.142323000000033\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['ENO', 'PUNP1', 'GDHm', 'PGM'], inactive_NC:['FTHFDH']\n", + "Reaction FTHFDH is not in Z\n", + "1442\n", + "1442\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 984 (119 core, 865 non-core); Num. remaining: 25\n", + "Reaction no. 953\n", + "Attempting to remove reaction: DNDPt20m ...\n", + "Initial PM reactions: 1442\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1059390000000349\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['HCO3_CLt'], inactive_NC:['DNDPt20m']\n", + "Reaction DNDPt20m is not in Z\n", + "1442\n", + "1442\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 984 (119 core, 865 non-core); Num. remaining: 24\n", + "Reaction no. 954\n", + "Attempting to remove reaction: DNDPt13m ...\n", + "Initial PM reactions: 1442\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.425296999999773\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['GLUt2m'], inactive_NC:['DNDPt13m']\n", + "Reaction DNDPt13m is not in Z\n", + "1442\n", + "1442\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 984 (119 core, 865 non-core); Num. remaining: 23\n", + "Reaction no. 955\n", + "Attempting to remove reaction: DNDPt32m ...\n", + "Initial PM reactions: 1442\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 0 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3932320000003529\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 1 , inactive_C: [], inactive_NC:['DNDPt32m']\n", + "Reaction DNDPt32m is not in Z\n", + "1442\n", + "1442\n", + "check_model_function done ....\n", + "Removed non-core inactive reactions\n", + "PM reactions (after): 1441\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 22\n", + "Reaction no. 956\n", + "Attempting to remove reaction: DNDPt19m ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1462339999998221\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['GLUt2m', 'LEUTAm'], inactive_NC:['DNDPt19m', 'LEUt5m']\n", + "Reaction DNDPt19m is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 21\n", + "Reaction no. 957\n", + "Attempting to remove reaction: FBP ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1456429999998363\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['PFK'], inactive_NC:['FBP']\n", + "Reaction FBP is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 20\n", + "Reaction no. 958\n", + "Attempting to remove reaction: ATPasel ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 180 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.9342079999996713\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 181 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'SOAT12', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'CREATt4_2_r', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'MEVK1x', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'NADPtxu', 'GACMTRc', 'DM_dctp_m', 'EX_estrones_e', 'EX_creat_e', 'DUDPtn', 'GLCt4', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'DNDPt56m', 'PA_HSter', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'GLYAMDTRc', 'CHSTEROLt2', 'NDP6', 'COAtp']\n", + "Reaction ATPasel is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 19\n", + "Reaction no. 959\n", + "Attempting to remove reaction: CITRtm ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4244669999998223\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['ARGSL', 'ARGSS', 'CBPSam', 'ARGNm', 'UREAt'], inactive_NC:['OCBTm', 'CITRtm', 'UREAtm', 'ARGtm', 'EX_urea_e']\n", + "Reaction CITRtm is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 18\n", + "Reaction no. 960\n", + "Attempting to remove reaction: ETFQO ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1210019999998622\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['HCO3_CLt', 'ETF'], inactive_NC:['ETFQO']\n", + "Reaction ETFQO is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 17\n", + "Reaction no. 961\n", + "Attempting to remove reaction: MI1PS ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 16\n", + "Reaction no. 962\n", + "Attempting to remove reaction: G6PPer ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 3 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.3929259999995338\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 4 , inactive_C: ['G6Pter', 'TRIODTHYt2'], inactive_NC:['G6PPer', 'TRIODTHYt']\n", + "Reaction G6PPer is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 15\n", + "Reaction no. 963\n", + "Attempting to remove reaction: 3AIBTm ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.395619999999326\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['NKCC2t', 'TRIODTHYt2'], inactive_NC:['3AIBtm', 'EX_3aib_e', '3AIBTm', '3AIBt', 'TRIODTHYt']\n", + "Reaction 3AIBTm is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 14\n", + "Reaction no. 964\n", + "Attempting to remove reaction: PPAer ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 94 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4524880000008125\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 95 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'EBP1r', 'HMGCOARx', 'MACACI', 'C4STMO1r', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'THYMDt1', 'GDHm', 'PSSA2_hs', 'CREATt4_2_r', 'TRIODTHYt2', 'C4STMO2Pr', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'DHCRD2', 'SQLSr', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'DHCR72r', 'DGAT', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'NDPK6n', 'LSTO1r', 'DHCR71r'], inactive_NC:['PPAer', 'NADPtxu', 'CEPTE', 'PA_HSter', 'GACMTRc', 'TRIODTHYt', 'AHCYStr', 'EX_creat_e', 'EX_thymd_e', 'AMETr', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'FORtr', 'DUMPtn', 'CHSTEROLt3', 'PItx', 'ATPtx', 'PEFLIP', '34HPPOR', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'GLYAMDTRc', 'PE_HSter', 'CHSTEROLt2', 'EX_pe_hs_e', 'EX_xolest_hs_e', 'XOLESTte', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction PPAer is not in Z\n", + "1441\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 13\n", + "Reaction no. 965\n", + "Attempting to remove reaction: SO4t4_2 ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 9 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4106599999995524\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 10 , inactive_C: ['GCALDD', 'FBA4', 'SO4HCOtex', 'OXAHCOtex', 'GLXO1'], inactive_NC:['SO4OXAtex2', 'SO4CLtex2', 'KHK2', 'EX_oxa_e', 'SO4t4_2']\n", + "Reaction SO4t4_2 is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 12\n", + "Reaction no. 966\n", + "Attempting to remove reaction: L_LACDcm ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 2 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.361417000000074\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 3 , inactive_C: ['HCO3_CLt', 'SERtN1'], inactive_NC:['L_LACDcm']\n", + "Reaction L_LACDcm is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 11\n", + "Reaction no. 967\n", + "Attempting to remove reaction: PDE4 ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.2312110000002576\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['HCO3_CLt', 'CREATt4_2_r', 'PUNP1'], inactive_NC:['GACMTRc', 'PDE4', 'EX_creat_e', 'GLYAMDTRc']\n", + "Reaction PDE4 is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 10\n", + "Reaction no. 968\n", + "Attempting to remove reaction: B_MANNASEly ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 189 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.8404400000008536\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 190 , inactive_C: ['C3STDH1Pr', 'EBP2r', 'PETOHMr_hs', 'EBP1r', 'NACHEX27ly', 'RNDR3', 'SOAT11', 'TYRTA', 'CERT1rt', 'SQLSr', 'C4STMO2r', 'DGAT', 'GLCAASE9ly', 'FUCASEe', 'ACNAM9PL2', 'SOAT12', 'GALUi', 'NDPK6n', 'DHCR71r', 'LNSTLSr', 'SMS', 'GRTTx', 'PGPPT', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'G6Pter', 'GLCURtly', 'FACOAL161', 'AACOAT', 'GLPASE2', 'TMDS', 'GLBRAN', 'UGLT', 'SBPP3er', 'GASNASE2ly', 'UDPGD', 'HMGCOAS', 'LNS14DMr', 'C14STRr', 'SIAASEly', 'GALASE1ly', 'HSD17B7r', 'CERT2rt', 'LSTO1r', 'DUTPDPn', 'AHEXASE2ly', 'FUMAC', 'GBA', 'DCYTD', 'PMEVKx', 'UDPDOLPT_L', 'DHCR241r', 'THYMDt1', 'C4STMO2Pr', 'LSTO2r', 'GLPASE1', 'ACACT1r_copy1', 'DHCR72r', 'HEX4', 'MEVK1x', 'A_MANASEly', 'SQLEr', 'SBPP1er', 'NTD3', 'IPDDIx', 'DPMVDx', 'AHEXASEly', 'ACNAMlt', 'UDPDOLPT_U', 'C3STDH1r', 'GLDBRAN', 'HSD17B8r', 'GGNG', 'GALKr', 'HMGCOARx', 'GLGNS1', 'UGCG', 'PSSA2_hs', 'DMATTx', 'DHCR242r', 'DHCRD2', 'GLCAASE8ly', 'GASNASEly', 'PETHCT', 'HSD17B9r', 'DHCR243r'], inactive_NC:['ENGASEly', 'PPAer', 'DOLGLCP_Uter', 'SLCBK1', 'PIter', 'DOLP_Uter', 'NDP7er', 'P4501B1r', 'SPHINGStr', 'EX_hestratriol_e', 'PCHOLPr_hs', 'UDPG4E', 'C3STKR2r', 'DUMPtn', 'PItx', 'PEFLIP', 'UDPGLCter', 'PPItx', 'DNDPt53m', 'UDPGNP', 'HSD3B2r', 'DNDPt51m', 'EX_xolest_hs_e', 'XOLESTte', 'CO2tp', 'MANtly', 'DM_kdn_c', 'NADPtxu', 'DM_dctp_m', 'EX_estrones_e', 'DUDPtn', 'HSD3A1r', 'NADHtru', 'GALtly', 'HMGCOAtx', 'SPH1Pter', 'EX_s2l2fn2m2masn_e', 'CHSTEROLt3', 'ATPtx', 'ESTRONEtr', 'HESTRATRIOLte', 'B_MANNASEly', 'SPHS1Ptr', 'FRDPtr', 'DOLK_L', 'DNDPt56m', 'PA_HSter', 'KDNH', 'HESTRATRIOLtr', 'CHOLtr', 'FADH2tru', 'DNDPt55m', 'PGPP_hs', 'GUR1PP', 'NADPHtxu', 'ENGASE2ly', 'CO2ter', 'DOLP_Lter', 'PROD2', 'UDPG1P', 'HGNTOR', 'ADPtx', 'FORtr', 'NADtru', 'HSD3B3r', 'DNDPt52m', '34HPPOR', 'ATPasel', 'THMDt4', 'biomass_mac', 'PE_HSter', 'EX_pe_hs_e', 'DNDPt54m', 'HAS1', 'O2ter', 'DOLPH_Ler', 'EX_n2m2nmasn_e', 'NADPtru', 'HAS2', 'CEPTE', 'DOLGPP_Uer', 'NADPHtru', 'AHCYStr', 'HAtly', 'SPHK21c', 'EX_thymd_e', 'AMETr', 'DOLICHOL_Lter', 'S2L2N2M2MASNtly', 'DOLGPP_Ler', 'GLCMter', 'FADtru', 'N2M2NMASNtly', 'G6PPer', 'DOLGLCP_Lter', 'ESTRONESt2', 'SPHGNtr', 'CHSTEROLt2', 'ACGAMtly', 'DM_Asn_X_Ser_Thr_l', 'NDP6', 'COAtp']\n", + "Reaction B_MANNASEly is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 9\n", + "Reaction no. 969\n", + "Attempting to remove reaction: ARGtm ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 14 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4346239999995305\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 15 , inactive_C: ['PGM', 'ARGSL', 'ARGSS', 'TRIODTHYt2', 'ENO', 'SERtN1', 'CBPSam', 'ARGNm', 'UREAt'], inactive_NC:['OCBTm', 'CITRtm', 'UREAtm', 'ARGtm', 'EX_urea_e', 'TRIODTHYt']\n", + "Reaction ARGtm is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 8\n", + "Reaction no. 970\n", + "Attempting to remove reaction: LRAT ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1309479999999894\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['CREATt4_2_r'], inactive_NC:['EX_creat_e', 'GLYAMDTRc', 'RETH', 'LRAT', 'GACMTRc']\n", + "Reaction LRAT is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 7\n", + "Reaction no. 971\n", + "Attempting to remove reaction: PHETHPTOX2 ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 5 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.0871159999996962\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 6 , inactive_C: ['GLUt2m', 'NKCC2t', 'MTHFD2m', 'TRIODTHYt2'], inactive_NC:['PHETHPTOX2', 'TRIODTHYt']\n", + "Reaction PHETHPTOX2 is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 6\n", + "Reaction no. 972\n", + "Attempting to remove reaction: GGLUCT ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 7 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.380620999999337\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 8 , inactive_C: ['AMPTASECG', 'AMPTASECGe', 'GTHS', 'CGLYt3_2'], inactive_NC:['GGLUCT', 'GTMLTe', 'GLUCYS', 'OPAH']\n", + "Reaction GGLUCT is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 5\n", + "Reaction no. 973\n", + "Attempting to remove reaction: PIter ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 130 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4770330000001195\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 131 , inactive_C: ['DUTPDPn', 'C3STDH1r', 'C3STDH1Pr', 'EBP2r', 'LNSTLSr', 'PETOHMr_hs', 'HSD17B8r', 'SMS', 'GRTTx', 'PGPPT', 'FUMAC', 'GBA', 'EBP1r', 'HMGCOARx', 'C4STMO1r', 'MACACI', 'NDPK7', 'RNDR4', 'DCYTD', 'PMEVKx', 'DHCR241r', 'UGCG', 'THYMDt1', 'RNDR3', 'PSSA2_hs', 'CREATt4_2_r', 'C4STMO2Pr', 'G6Pter', 'DMATTx', 'SOAT11', 'TYRTA', 'FACOAL161', 'DHCR242r', 'AACOAT', 'CERT1rt', 'SQLSr', 'DHCRD2', 'TMDS', 'PETHCT', 'LSTO2r', 'C4STMO2r', 'ACACT1r_copy1', 'SBPP3er', 'DGAT', 'DHCR72r', 'HMGCOAS', 'MEVK1x', 'LNS14DMr', 'C14STRr', 'SQLEr', 'SBPP1er', 'NTD3', 'DHCR243r', 'IPDDIx', 'SOAT12', 'DPMVDx', 'HSD17B7r', 'NDPK6n', 'CERT2rt', 'LSTO1r', 'DHCR71r'], inactive_NC:['DOLPH_Ler', 'PPAer', 'DNDPt56m', 'NADPtxu', 'CEPTE', 'PA_HSter', 'SLCBK1', 'PIter', 'NDP7er', 'GACMTRc', 'DM_dctp_m', 'EX_estrones_e', 'AHCYStr', 'EX_creat_e', 'P4501B1r', 'SPHK21c', 'SPHINGStr', 'HESTRATRIOLtr', 'EX_thymd_e', 'CHOLtr', 'DUDPtn', 'FADH2tru', 'AMETr', 'GLCt4', 'EX_hestratriol_e', 'DNDPt55m', 'DOLICHOL_Lter', 'PCHOLPr_hs', 'PGPP_hs', 'NADPHtxu', 'CO2ter', 'PROD2', 'FADtru', 'HGNTOR', 'HMGCOAtx', 'ADPtx', 'C3STKR2r', 'SPH1Pter', 'FORtr', 'DUMPtn', 'G6PPer', 'CHSTEROLt3', 'PItx', 'ATPtx', 'DNDPt52m', 'ESTRONESt2', 'PEFLIP', 'ESTRONEtr', 'HESTRATRIOLte', 'SPHS1Ptr', '34HPPOR', 'UDPGLCter', 'PPItx', 'FRDPtr', 'THMDt4', 'biomass_mac', 'DNDPt53m', 'PE_HSter', 'SPHGNtr', 'GLYAMDTRc', 'CHSTEROLt2', 'DOLK_L', 'EX_pe_hs_e', 'DNDPt51m', 'DNDPt54m', 'EX_xolest_hs_e', 'XOLESTte', 'NDP6', 'CO2tp', 'COAtp']\n", + "Reaction PIter is not in Z\n", + "1441\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 4\n", + "Reaction no. 974\n", + "Attempting to remove reaction: PRO1xm ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 4 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1163400000004913\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 5 , inactive_C: ['GLUt2m', 'PUNP1', 'LEUTAm'], inactive_NC:['LEUt5m', 'PRO1xm']\n", + "Reaction PRO1xm is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 3\n", + "Reaction no. 975\n", + "Attempting to remove reaction: PROD2m ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 6 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4186510000008639\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 7 , inactive_C: ['MTHFC', 'PUNP1', 'TRIODTHYt2', 'MTHFD'], inactive_NC:['EX_pi_e', 'PROD2m', 'TRIODTHYt']\n", + "Reaction PROD2m is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 2\n", + "Reaction no. 976\n", + "Attempting to remove reaction: PPCOACm ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 30 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.4242819999999483\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 31 , inactive_C: ['HPDCACRNCPT1', 'ACOAD10m', 'OIVD3m', 'FACOAL170', 'FACOAL150', 'MMEm', 'LEUTAm', 'PTDCACRNCPT1', 'FAOXC170m', 'GLUt2m', 'PTDCACRNt', 'HPDCACRNt', 'HACD9m', 'HPDCACRNCPT2', 'ECOAH9m', 'PTDCACRNCPT2', 'FAOXC150m'], inactive_NC:['MMSAD1m', 'PPAtm', 'EX_hpdca_e', 'ILETA', 'ACACT10m', 'PTDCAt', 'HPDCAt', 'GLCt4', '3MOPt2im', 'EX_ptdca_e', 'PPCOACm', 'LEUt5m', 'ACCOALm', 'MMCDm']\n", + "Reaction PPCOACm is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 1\n", + "Reaction no. 977\n", + "Attempting to remove reaction: PIt2m ...\n", + "Initial PM reactions: 1441\n", + "check_model_function done ....\n", + "Checking all reactions (FASTCC)...\n", + "Model consists of 1 blocked (inactive) reactions\n", + "Execution time of check_model_consistency: 1.1086519999998927\n", + "check_model_consistency done ... \n", + "Lengths all--> inactive_G: 2 , inactive_C: ['MTHFD2m'], inactive_NC:['PIt2m']\n", + "Reaction PIt2m is not in Z\n", + "1441\n", + "1441\n", + "check_model_function done ....\n", + "No reactions removed\n", + "Num. removed: 985 (119 core, 866 non-core); Num. remaining: 0\n", + "prune_model done .... \n" + ] + } + ], + "source": [ + "from prune.prune_model import *\n", + "print('Generic model passed precursor metabolites test')\n", + "\n", + "##############################################################\n", + "# If generic functionality test is passed, prune reactions\n", + "###############################################################\n", + "print('Pruning reactions...')\n", + "t0 = process_time()\n", + "PM, cRes = prune_model(GM, P, C, Z, 1/3, '../../test_dataset/key_metabolites_RECON1.txt', 1, 2)\n", + "# Stop the stopwatch / counter\n", + "t_stop = process_time()\n", + "# compute elapsed time\n", + "pruneTime = t_stop - t0" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "1441" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(PM.reactions)" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "1100" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(PM.metabolites)" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "1160" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(PM.genes)" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "7080.335198" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pruneTime" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "#cores and non-cores\n", + "#985 (119 core, 866 non-core)" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [], + "source": [ + "# save model\n", + "io.write_sbml_model(PM,\"python_recon1_with_BOF_and_VBOF_method2.xml\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.4" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/pymcadre/test_scripts/test_check_model_consistency_module.ipynb b/pymcadre/test_scripts/test_check_model_consistency_module.ipynb new file mode 100644 index 0000000..42d9cfd --- /dev/null +++ b/pymcadre/test_scripts/test_check_model_consistency_module.ipynb @@ -0,0 +1,283 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "db03b1bf", + "metadata": {}, + "outputs": [], + "source": [ + "from prune.check_core_deadends import *\n", + "from prune.find_inactive_rxns import *\n", + "from cobra import *" + ] + }, + { + "cell_type": "markdown", + "id": "f9869463", + "metadata": {}, + "source": [ + "### Test check_core_dead_ends" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2e3e7d2d", + "metadata": {}, + "outputs": [], + "source": [ + "print('## Testing check_core_dead_ends...')\n", + "\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "C=['P4504B1r','SO4HCOtex','A_MANASEly','SPMS','ILETA','AGPRim','ESTRIOLtr','GLU5Km','UAG4Ei','UDPGLCter','CITtbm','UGALGTg',\n", + "'THRt4','FRUt4','PROD2m','BILGLCURtr','ARTFR55','SPHMYLNtl','PI3P3Pn','THYMDtl','MESCOALm','ABUTt2r','RTOT_2','TDCHOLAte',\n", + "'MI4PP','NTD5m','NRPPHRtu','EX_rbt_e','MEPIVESSte','CYSt4','NABTNO','3HPPD','ENMAN2g','AASAD3m','AGMTm','PPDOy','NACHEX9ly',\n", + "'EX_acn13acngalgbside_hs_e','STRDNCCPT2','6DHFtm','EX_xolest2_hs_e','EX_lac__L_e','PCm','PI34P4Pn','DM_ethamp_r','FT',\n", + "'FAOXC2252053m','INOSTO','TMNDNCCPT1','NTD1m','ELAIDCRNt','MI1PP','KSII_CORE4t','CSPG_Bt','ANDRSTRNtr','FUCACGALFUCGALACGLCGALGLUSIDEtg',\n", + "'TTDCRNt','EX_dmhptcrn_e','GALACGLCGALGBSIDEtg','COAtp','LGNCCOAtx','DIGALSGALSIDEte','GASNASEly','NACHEX6ly','PA_HSter']\n", + "\n", + "\n", + "try:\n", + "\n", + " deadEnd_C = check_core_dead_ends(model, C)\n", + " \n", + " if len(deadEnd_C) == 1 and 'P4504B1r' in deadEnd_C:\n", + "\n", + " print('Function returns the [expected] result: %s dead-end reactions' %len(deadEnd_C))\n", + "\n", + " else:\n", + "\n", + " print('Function returns the [unexpected] result: %s dead-end reactions' %len(deadEnd_C))\n", + "\n", + " \n", + " print('PASS...', 'Function find_ex_rxns ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function check_core_deadends was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "markdown", + "id": "a1e9275a", + "metadata": {}, + "source": [ + "#### Test with small core which should contain no dead-end metabolites" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e4ec7acc", + "metadata": {}, + "outputs": [], + "source": [ + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "\n", + "C = ['EX_glc__D_e']\n", + "\n", + "print(\"## Testing check_core_deadends with small core...\")\n", + "try:\n", + "\n", + " deadEnd_C = check_core_dead_ends(model, C)\n", + " \n", + " if len(deadEnd_C) == 0:\n", + "\n", + " print('Function returns the [expected] result')\n", + "\n", + " else:\n", + "\n", + " print('Function returns the [unexpected] result')\n", + "\n", + " \n", + " print('PASS...', 'Function find_ex_rxns ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function check_core_deadends was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "markdown", + "id": "eed5a1f5", + "metadata": {}, + "source": [ + "### Test find_inactive_rxns" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d7d97fe9", + "metadata": {}, + "outputs": [], + "source": [ + "print('## Testing find_inactive_rxns...')\n", + "\n", + "\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml') # read model from SBML file\n", + "\n", + "try:\n", + "\n", + " fast_fva = find_inactive_rxns(model)\n", + " \n", + " if len(fast_fva) == 1272:\n", + "\n", + " print('Function returns the [expected] result: %s inactive reactions' %len(fast_fva))\n", + "\n", + " else:\n", + "\n", + " print('Function returns the [unexpected] result: %s inactive reactions' %len(fast_fva))\n", + "\n", + " \n", + " print('PASS...', 'Function find_ex_rxns ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function find_inactive_rxns was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1c58c266", + "metadata": {}, + "outputs": [], + "source": [ + "# fastcc delivers each time different results. Thus, cannot be properly tested" + ] + }, + { + "cell_type": "markdown", + "id": "ca71a98b", + "metadata": {}, + "source": [ + "### Test check_model_consistency" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "15dc9cd3", + "metadata": {}, + "outputs": [], + "source": [ + "from time import process_time\n", + "from prune.check_model_consistency import *\n", + "\n", + "print('## Testing check_model_consistency...')\n", + "\n", + "\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml') # read model from SBML file\n", + "\n", + "\n", + "try:\n", + "\n", + " check_consistency = check_model_consistency(model,1) \n", + " \n", + " if len(check_consistency[0]) == 1272: # should find 1272 blocked reactions in Recon1\n", + "\n", + " print('Function returns the [expected] result')\n", + "\n", + " else:\n", + "\n", + " print('Function returns the [unexpected] result')\n", + "\n", + " \n", + " print('PASS...', 'Function check_model_consistency ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function check_model_consistency was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "markdown", + "id": "90d724d8", + "metadata": {}, + "source": [ + "#### Test with fastFVA, using consistent model + removed reaction" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0dc00427", + "metadata": {}, + "outputs": [], + "source": [ + "r = 'ACCOAC'\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml') # read model from SBML file\n", + "\n", + "try:\n", + "\n", + " check_consistency = check_model_consistency(model,1,rxn_to_remove=[r])\n", + " \n", + " if len(check_consistency[0]) == 1285: # should find 13 inactive rxns in Recon1-consistent\n", + "\n", + " print('Function returns the [expected] result')\n", + "\n", + " else:\n", + "\n", + " print('Function returns the [unexpected] result', len(check_consistency[0]))\n", + "\n", + " \n", + " print('PASS...', 'Function check_model_consistency ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function check_model_consistency was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b87f8be6", + "metadata": {}, + "outputs": [], + "source": [ + "model" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6b39a75d", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/pymcadre/test_scripts/test_check_module.ipynb b/pymcadre/test_scripts/test_check_module.ipynb new file mode 100644 index 0000000..3addfa8 --- /dev/null +++ b/pymcadre/test_scripts/test_check_module.ipynb @@ -0,0 +1,315 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "099bd8c2", + "metadata": {}, + "outputs": [], + "source": [ + "from check.find_ex_reactions import *\n", + "from check.set_metabolite_bounds import *\n", + "from check.find_required_rxns import *\n", + "from check.check_rxn_flux import *\n", + "from cobra import *" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ebdc26be", + "metadata": {}, + "outputs": [], + "source": [ + "precursorMets = '../pre_processing/dataset/key_metabolites_RECON1.txt'" + ] + }, + { + "cell_type": "markdown", + "id": "5be344a2", + "metadata": {}, + "source": [ + "### Test find_ex_reactions.py" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "da1ea2ef", + "metadata": {}, + "outputs": [], + "source": [ + "print('## Testing find_ex_reactions...')\n", + "\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "\n", + "try:\n", + "\n", + " exRxns = find_ex_rxns(model)\n", + " \n", + " if len(exRxns) == 430:\n", + "\n", + " print('Function returns the [expected] result: %s exchange & demand reactions' %len(exRxns))\n", + "\n", + " else:\n", + "\n", + " print('Function returns the [unexpected] result: %s exchange & demand reactions' %len(exRxns))\n", + "\n", + " \n", + " print('PASS...', 'Function find_ex_rxns ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function find_ex_rxns was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "markdown", + "id": "d1e6ce4d", + "metadata": {}, + "source": [ + "### Test find_organic_ex_rxns.py" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "33d37de5", + "metadata": {}, + "outputs": [], + "source": [ + "display('## Testing find_organic_ex_rxns...');\n", + "\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "\n", + "try:\n", + " organicExRxns = find_organic_ex_rxns(model, exRxns)\n", + " \n", + " if len(organicExRxns) == 406:\n", + " \n", + " print('Function returns the [expected] result: %s organic reactions' %len(organicExRxns))\n", + " \n", + " else:\n", + " \n", + " print('Function returns the [unexpected] result: %s organic reactions' %len(organicExRxns))\n", + "\n", + " \n", + " print('PASS...', 'Function find_organic_ex_rxns ran without error')\n", + " \n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + " \n", + " print('FAIL...', 'Function find_organic_ex_rxns was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "markdown", + "id": "ea74cf69", + "metadata": {}, + "source": [ + "### Test set_metabolite_bounds.py" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4ab46385", + "metadata": {}, + "outputs": [], + "source": [ + "display('## Testing set_organic_met_bounds...');\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "try:\n", + " testModel = set_organic_met_bounds(model, exRxns)\n", + " print('PASS...', 'Function set_organic_met_bounds ran without error')\n", + " \n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + " \n", + " print('FAIL...', 'Function set_organic_met_bounds was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)\n", + " \n", + "# check all bounds were set correctly\n", + "print(\"## Testing output of set_organic_met_bounds...\")\n", + "# check if all organic reactions are in model\n", + "for r in organicExRxns:\n", + " if testModel.reactions.get_by_id(r).lower_bound != 0:\n", + " print(\"Bound for [%s] not set correctly\" %r)" + ] + }, + { + "cell_type": "markdown", + "id": "93aa615e", + "metadata": {}, + "source": [ + "### Test find_required_rxns.py" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "24d8e1a0", + "metadata": {}, + "outputs": [], + "source": [ + "display('## Testing find_required_rxns...');\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "try:\n", + " testModel, requiredRxns = find_required_rxns(model, '../pre_processing/dataset/key_metabolites_RECON1.txt')\n", + " print('PASS...', 'Function find_required_rxns ran without error')\n", + " \n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + " \n", + " print('FAIL...', 'Function find_required_rxns was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "markdown", + "id": "bcf9c328", + "metadata": {}, + "source": [ + "### Test check_rxn_flux.py" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "70370adc", + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "print('## Checking for success on preceding tests...')\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "try:\n", + " \n", + " metList = precursorMets\n", + " exRxns = find_ex_rxns(model)\n", + " testModel = set_organic_met_bounds(model, exRxns)\n", + " \n", + " \n", + " testModel, requiredRxns = find_required_rxns(model, metList)\n", + "\n", + " # Allow uptake of glucose and CO2\n", + " testModel.reactions.get_by_id(\"EX_glc__D_e\").lower_bound = -5 \n", + " testModel.reactions.get_by_id(\"EX_co2_e\").lower_bound = -1000 \n", + "\n", + " \n", + "except(RuntimeError, TypeError, NameError) as inst:\n", + " \n", + " print('FAIL...', 'Cannot test check_rxn_flux because one of the preceding functions returned the error:')\n", + " print(type(inst))\n", + " print(inst.args)\n", + " \n", + "# Test whether Recon1 passes functional check \n", + "print('## Testing check_rxn_flux with functional input...') \n", + "\n", + "try:\n", + " inactiveRequired = check_rxn_flux(testModel, requiredRxns)\n", + " print('PASS...','Function check_rxn_flux ran without error')\n", + " \n", + "except(RuntimeError, TypeError, NameError) as inst:\n", + " \n", + " print('FAIL...', 'Function check_rxn_flux was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)\n", + " \n", + "# Test if Recon 1 passes check when you 'break' it (turn off glucose)\n", + "print('## Testing check_rxn_flux with glucose uptake off...')\n", + "try:\n", + " with testModel:\n", + " testModel.reactions.get_by_id(\"EX_glc__D_e\").lower_bound == 0\n", + " inactiveRequired = check_rxn_flux(testModel, requiredRxns)\n", + " print('PASS...', 'Function check_rxn_flux ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + " \n", + " print('FAIL...', 'Function check_rxn_flux was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)\n", + " \n", + "\n", + "# Test if Recon 1 passes check when you 'break' it (output blocked) \n", + "print('## Testing check_rxn_flux with one output blocked...')\n", + "try:\n", + " with testModel:\n", + " testModel.reactions.get_by_id(\"DM_3pg_c\").upper_bound == 0\n", + " inactiveRequired = check_rxn_flux(testModel, requiredRxns)\n", + " print('PASS...', 'Function check_rxn_flux ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + " \n", + " print('FAIL...', 'Function check_rxn_flux was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "markdown", + "id": "93c421a1", + "metadata": {}, + "source": [ + "### Test check_model_function.py" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c6dc3f5a", + "metadata": {}, + "outputs": [], + "source": [ + "from check.check_model_function import *\n", + "# test with default inputs\n", + "print('## Testing check_model_function with default inputs...')\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "\n", + "try:\n", + " \n", + " genericStatus = check_model_function(model,'requiredMets', precursorMets)\n", + " print('PASS...', 'Function check_model_function ran without error')\n", + " \n", + " if genericStatus:\n", + " print('PASS...', \n", + " 'Check for functionality returns expected result')\n", + " else:\n", + " print('FAIL...', \n", + " 'Check for functionality returns unexpected result')\n", + " \n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + " \n", + " print('FAIL...', 'Function check_model_function was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)\n", + " " + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/pymcadre/test_scripts/test_prune_model_fastcc.ipynb b/pymcadre/test_scripts/test_prune_model_fastcc.ipynb new file mode 100644 index 0000000..8f11d1b --- /dev/null +++ b/pymcadre/test_scripts/test_prune_model_fastcc.ipynb @@ -0,0 +1,168 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "38f8d682", + "metadata": {}, + "source": [ + "## fastcc" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "efa9759c", + "metadata": {}, + "outputs": [], + "source": [ + "__author__ = \"Nantia Leonidou\"\n", + "__description__ = \" Main script \"\n", + "\n", + "import pandas as pd\n", + "import numpy as np\n", + "from rank.rank_reactions import *\n", + "from prune.prune_model import *" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "060f391c", + "metadata": {}, + "outputs": [], + "source": [ + "# read model\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "# genes\n", + "G = pd.read_csv('../pre_processing/dataset/1_GPL570_GSE3397/1_GPL570_GSE3397_entrez_ids.csv')\n", + "G = list(G['ENTREZ_GENE_ID'])\n", + "# ubiquity scores\n", + "U = pd.read_csv('../pre_processing/dataset/1_GPL570_GSE3397/1_GPL570_GSE3397_ubiquity.csv', header=None)\n", + "U = U.rename(columns={0: \"Scores\"})\n", + "U = list(U['Scores'])\n", + "#confidence_scores\n", + "#confidence_scores = get_test_inputs('../testInputs.mat','../humanModel.mat')[3]\n", + "#confidence_scores[-1] = 4\n", + "confidence_scores = pd.read_csv('../pre_processing/dataset/Recon1_confidence_scores_with_BOF_and_VBOF.csv')\n", + "confidence_scores = np.float64(list(confidence_scores['Confidence Score']))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "dc95943d", + "metadata": {}, + "outputs": [], + "source": [ + "GM, C, NC, P, Z, model_C = rank_reactions(model, G, U, confidence_scores, [], 2) " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2b6fd499", + "metadata": {}, + "outputs": [], + "source": [ + "print(len(GM.reactions))\n", + "print(len(GM.metabolites))\n", + "print(len(GM.genes))\n", + "print(len(C))\n", + "print(len(NC))\n", + "print(len(P))\n", + "print(len(Z))\n", + "print(len(model_C))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b7979a3d", + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "print('Generic model passed precursor metabolites test')\n", + "\n", + "##############################################################\n", + "# If generic functionality test is passed, prune reactions\n", + "###############################################################\n", + "try:\n", + " \n", + " print('Pruning reactions...')\n", + " t0 = process_time()\n", + " PM, cRes = prune_model(GM, P, C, Z, 1/3, '../pre_processing/dataset/key_metabolites_RECON1.txt', 1, 2)\n", + " # Stop the stopwatch / counter\n", + " t_stop = process_time()\n", + " # compute elapsed time\n", + " pruneTime = t_stop - t0\n", + " \n", + " print('PASS...', 'Function prune_model ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function prune_model was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9eb8b6af", + "metadata": {}, + "outputs": [], + "source": [ + "print(len(PM.reactions))\n", + "print(len(PM.metabolites))\n", + "print(len(PM.genes))\n", + "print(len(cRes))\n", + "print(pruneTime)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1956745f", + "metadata": {}, + "outputs": [], + "source": [ + "hours, rem = divmod(t_stop-t0, 3600)\n", + "minutes, seconds = divmod(rem, 60)\n", + "print(\"{:0>2}:{:0>2}:{:05.2f}\".format(int(hours),int(minutes),seconds))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2f4f1f7b", + "metadata": {}, + "outputs": [], + "source": [ + "io.write_sbml_model(PM,\"final_python_recon1_with_BOF_BEC1_method2.xml\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/pymcadre/test_scripts/test_prune_module_fastFVA.ipynb b/pymcadre/test_scripts/test_prune_module_fastFVA.ipynb new file mode 100644 index 0000000..c055eaa --- /dev/null +++ b/pymcadre/test_scripts/test_prune_module_fastFVA.ipynb @@ -0,0 +1,168 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "646b0456", + "metadata": {}, + "outputs": [], + "source": [ + "__author__ = \"Nantia Leonidou\"\n", + "__description__ = \" Main script \"\n", + "\n", + "import pandas as pd\n", + "import numpy as np\n", + "from rank.rank_reactions import *\n", + "from prune.prune_model import *" + ] + }, + { + "cell_type": "markdown", + "id": "5c7216cd", + "metadata": {}, + "source": [ + "## fastFVA" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c69075ee", + "metadata": {}, + "outputs": [], + "source": [ + "# read model\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "# genes\n", + "G = pd.read_csv('../pre_processing/dataset/1_GPL570_GSE3397/1_GPL570_GSE3397_entrez_ids.csv')\n", + "G = list(G['ENTREZ_GENE_ID'])\n", + "# ubiquity scores\n", + "U = pd.read_csv('../pre_processing/dataset/1_GPL570_GSE3397/1_GPL570_GSE3397_ubiquity.csv', header=None)\n", + "U = U.rename(columns={0: \"Scores\"})\n", + "U = list(U['Scores'])\n", + "#confidence_scores\n", + "#confidence_scores = get_test_inputs('../testInputs.mat','../humanModel.mat')[3]\n", + "#confidence_scores[-1] = 4\n", + "confidence_scores = pd.read_csv('../pre_processing/dataset/Recon1_confidence_scores_with_BOF_and_VBOF.csv')\n", + "confidence_scores = np.float64(list(confidence_scores['Confidence Score']))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1f08210f", + "metadata": {}, + "outputs": [], + "source": [ + "GM, C, NC, P, Z, model_C = rank_reactions(model, G, U, confidence_scores, [], 1)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f15053d3", + "metadata": {}, + "outputs": [], + "source": [ + "print(len(GM.reactions))\n", + "print(len(GM.metabolites))\n", + "print(len(GM.genes))\n", + "print(len(C))\n", + "print(len(NC))\n", + "print(len(P))\n", + "print(len(Z))\n", + "print(len(model_C))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "947767c9", + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "print('Generic model passed precursor metabolites test')\n", + "\n", + "##############################################################\n", + "# If generic functionality test is passed, prune reactions\n", + "###############################################################\n", + "try:\n", + " \n", + " print('Pruning reactions...')\n", + " t0 = process_time()\n", + " PM, cRes = prune_model(GM, P, C, Z, 1/3, '../pre_processing/dataset/key_metabolites_RECON1.txt', 1, 1)\n", + " # Stop the stopwatch / counter\n", + " t_stop = process_time()\n", + " # compute elapsed time\n", + " pruneTime = t_stop - t0\n", + " \n", + " print('PASS...', 'Function prune_model ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function prune_model was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "045859f1", + "metadata": {}, + "outputs": [], + "source": [ + "print(len(PM.reactions))\n", + "print(len(PM.metabolites))\n", + "print(len(PM.genes))\n", + "print(len(cRes))\n", + "print(pruneTime)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "06ed49f8", + "metadata": {}, + "outputs": [], + "source": [ + "hours, rem = divmod(19989.509817, 3600)\n", + "minutes, seconds = divmod(rem, 60)\n", + "print(\"{:0>2}:{:0>2}:{:05.2f}\".format(int(hours),int(minutes),seconds))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3fc99734", + "metadata": {}, + "outputs": [], + "source": [ + "io.write_sbml_model(PM,\"test_fastFVA.xml\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/pymcadre/test_scripts/test_rank_reactions_module.ipynb b/pymcadre/test_scripts/test_rank_reactions_module.ipynb new file mode 100644 index 0000000..b5eb740 --- /dev/null +++ b/pymcadre/test_scripts/test_rank_reactions_module.ipynb @@ -0,0 +1,365 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "36dc6e17", + "metadata": {}, + "outputs": [], + "source": [ + "from cobra import *\n", + "import pandas as pd\n", + "import numpy as np" + ] + }, + { + "cell_type": "markdown", + "id": "cbb981df", + "metadata": {}, + "source": [ + "### Test parse_gprs" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b474f81e", + "metadata": {}, + "outputs": [], + "source": [ + "from rank.parse_gprs import *\n", + "print('## Testing parse_gprs..')\n", + "\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "\n", + "try:\n", + "\n", + " parseGPRS = parse_gprs(model)\n", + " \n", + " GPR_rxns = parseGPRS[0]\n", + " GPR_file = parseGPRS[1]\n", + " \n", + " if (len(GPR_rxns) != 5962) and (len(GPR_file) != 5962):\n", + " \n", + " print('Function returns the [unexpected] result')\n", + "\n", + " \n", + " print('PASS...', 'Function parse_gprs ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function parse_gprs was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "markdown", + "id": "9c3ebb94", + "metadata": {}, + "source": [ + "### Test map_high_conf_to_rxns" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3c6607be", + "metadata": {}, + "outputs": [], + "source": [ + "from rank.map_high_conf_to_rxns import *\n", + "print('## Testing map_high_conf_to_rxns..')\n", + "\n", + "try:\n", + "\n", + " is_C_H = map_high_conf_to_rxns(model, GPR_file, GPR_rxns, [])\n", + " \n", + " \n", + " if len(is_C_H) != 3743:\n", + " \n", + " print('Function returns the [unexpected] result:' , len(is_C_H))\n", + "\n", + " \n", + " print('PASS...', 'Function map_high_conf_to_rxns ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function map_high_conf_to_rxns was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "markdown", + "id": "981f623e", + "metadata": {}, + "source": [ + "### Test map_gene_scores_to_rxns" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "632e4a8c", + "metadata": {}, + "outputs": [], + "source": [ + "from rank.map_gene_scores_to_rxns import *\n", + "\n", + "# genes\n", + "G = pd.read_csv('../pre_processing/dataset/1_GPL570_GSE3397/1_GPL570_GSE3397_entrez_ids.csv')\n", + "G = list(G['ENTREZ_GENE_ID'])\n", + "# ubiquity scores\n", + "U = pd.read_csv('../pre_processing/dataset/1_GPL570_GSE3397/1_GPL570_GSE3397_ubiquity.csv', header=None)\n", + "U = U.rename(columns={0: \"Scores\"})\n", + "U = list(U['Scores'])\n", + "\n", + "print('## Testing map_gene_scores_to_rxns..')\n", + "\n", + "\n", + "try:\n", + "\n", + " U_GPR = map_gene_scores_to_rxns(model, G, U, GPR_file)\n", + " \n", + " \n", + " if len(U_GPR) != 5962:\n", + "\n", + " print('Function returns the [unexpected] result', len(U_GPR))\n", + "\n", + " \n", + " print('PASS...', 'Function map_gene_scores_to_rxns ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function map_gene_scores_to_rxns was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "markdown", + "id": "28695cab", + "metadata": {}, + "source": [ + "### Test calc_expr_evidence" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c0a0f628", + "metadata": {}, + "outputs": [], + "source": [ + "from rank.calc_expr_evidence import *\n", + "\n", + "print('## Testing calc_expr_evidence..')\n", + "\n", + "\n", + "try:\n", + "\n", + " E_X = calc_expr_evidence(model, GPR_rxns, U_GPR,is_C_H)\n", + " \n", + " \n", + " if len(E_X) != 3743:\n", + "\n", + "\n", + " print('Function returns the [unexpected] result', len(E_X))\n", + "\n", + " \n", + " print('PASS...', 'Function calc_expr_evidence ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function calc_expr_evidence was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)" + ] + }, + { + "cell_type": "markdown", + "id": "61006330", + "metadata": {}, + "source": [ + "### Test initialize_generic_model" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b6212db4", + "metadata": {}, + "outputs": [], + "source": [ + "C = []\n", + "for i in range(len(E_X)):\n", + " if E_X[i] > 0.9:\n", + " C.append(model.reactions[i].id)\n", + "confidence_scores = pd.read_csv('../pre_processing/dataset/Recon1_confidence_scores_with_BOF_and_VBOF.csv')\n", + "confidence_scores = np.float64(list(confidence_scores['Confidence Score']))\n", + "\n", + "from rank.initialize_generic_model import *\n", + "\n", + "print('## Testing initialize_generic_model..')\n", + "\n", + "\n", + "try:\n", + "\n", + " GM, C, E_X, E_L = initialize_generic_model(model,C,E_X,confidence_scores,1)\n", + " \n", + " \n", + " if len(GM.reactions) != 2471:\n", + "\n", + "\n", + " print('Function returns the [unexpected] result', len(GM.reactions))\n", + " \n", + " \n", + " elif len(C) != 860:\n", + "\n", + "\n", + " print('Function returns the [unexpected] result', len(C))\n", + " \n", + " \n", + " elif len(E_X) != 2471:\n", + "\n", + "\n", + " print('Function returns the [unexpected] result', len(E_X))\n", + " \n", + " elif len(E_L) != 2471:\n", + "\n", + "\n", + " print('Function returns the [unexpected] result', len(E_L))\n", + "\n", + " else:\n", + " \n", + " print('Function returns the expected result')\n", + " \n", + " print('PASS...', 'Function initialize_generic_model ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function initialize_generic_model was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)\n" + ] + }, + { + "cell_type": "markdown", + "id": "def6a532", + "metadata": {}, + "source": [ + "### Test rank_reactions" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8530a1b5", + "metadata": {}, + "outputs": [], + "source": [ + "from rank.rank_reactions import *\n", + "\n", + "import pandas as pd\n", + "import numpy as np\n", + "\n", + "# read model\n", + "model = io.read_sbml_model('../pre_processing/dataset/recon1_with_BOF_and_VBOF.xml')\n", + "# genes\n", + "G = pd.read_csv('../pre_processing/dataset/1_GPL570_GSE3397/1_GPL570_GSE3397_entrez_ids.csv')\n", + "G = list(G['ENTREZ_GENE_ID'])\n", + "# ubiquity scores\n", + "U = pd.read_csv('../pre_processing/dataset/1_GPL570_GSE3397/1_GPL570_GSE3397_ubiquity.csv', header=None)\n", + "U = U.rename(columns={0: \"Scores\"})\n", + "U = list(U['Scores'])\n", + "#confidence_scores\n", + "#confidence_scores = get_test_inputs('../testInputs.mat','../humanModel.mat')[3]\n", + "#confidence_scores[-1] = 4\n", + "confidence_scores = pd.read_csv('../pre_processing/dataset/Recon1_confidence_scores_with_BOF_and_VBOF.csv')\n", + "confidence_scores = np.float64(list(confidence_scores['Confidence Score']))\n", + "\n", + "print('## Testing rank_reactions..')\n", + "\n", + "\n", + "try:\n", + "\n", + " GM, C, NC, P, Z, model_C = rank_reactions(model, G, U, confidence_scores, [], 1)\n", + " \n", + " if len(GM.reactions) != 2471:\n", + "\n", + "\n", + " print('Function returns the [unexpected] result', len(GM.reactions))\n", + " \n", + " \n", + " elif len(C) != 860:\n", + "\n", + "\n", + " print('Function returns the [unexpected] result', len(C))\n", + " \n", + " \n", + " elif len(NC) != 1611:\n", + "\n", + "\n", + " print('Function returns the [unexpected] result', len(NC))\n", + " \n", + " elif len(P) != 1611:\n", + "\n", + "\n", + " print('Function returns the [unexpected] result', len(P))\n", + "\n", + " elif len(Z) != 473:\n", + "\n", + "\n", + " print('Function returns the [unexpected] result', len(Z))\n", + " \n", + " \n", + " elif len(model_C) != 1322:\n", + "\n", + "\n", + " print('Function returns the [unexpected] result', len(model_C))\n", + " \n", + " else:\n", + " \n", + " print('Function returns the expected result')\n", + " \n", + " print('PASS...', 'Function rank_reactions ran without error')\n", + "\n", + "except (RuntimeError, TypeError, NameError) as inst:\n", + "\n", + " print('FAIL...', 'Function rank_reactions was terminated with the error:')\n", + " print(type(inst))\n", + " print(inst.args)\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e42ea634", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}