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pipeline fails when parameter trim = false #55

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2 of 5 tasks
craigwindell opened this issue Jun 27, 2022 · 2 comments
Open
2 of 5 tasks

pipeline fails when parameter trim = false #55

craigwindell opened this issue Jun 27, 2022 · 2 comments
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@craigwindell
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craigwindell commented Jun 27, 2022 •
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Check Documentation

I have checked the following places for your error:

Description of the bug

When setting trim = false, the pipeline stops with the error:

Jun-27 17:04:36.559 [main] ERROR nextflow.cli.Launcher - Access to 'FASTP.out' is undefined since the process 'FASTP' has not been invoked before accessing the output attribute
nextflow.exception.ScriptRuntimeException: Access to 'FASTP.out' is undefined since the process 'FASTP' has not been invoked before accessing the output attribute

Steps to reproduce

Steps to reproduce the behaviour:

  1. nextflow run nf-core/bactmap -profile singularity
  2. nextflow.config
...
    trim       = false
...
  1. See error: as above

Expected behaviour

When using already trimmed samples, we should be able to run bactmap with trim = false

Log files

Have you provided the following extra information/files:

  • The command used to run the pipeline
#!/bin/bash -l
#PBS -N bactmaptest
#PBS -l select=1:ncpus=2:mem=5gb
#PBS -l walltime=168:00:00

cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'

nextflow run nf-core/bactmap -profile singularity
  • nextflow.config
params {
    max_memory = '2.GB'
    max_cpus   = 2
    max_time   = '1.h'
    rapidnj    = true
    fasttree   = true
    iqtree     = true
    raxmlng    = true
    trim       = false
    input      = 'samplesheet.csv'
    reference  = 'NCTC13799.fna'
}
  • The .nextflow.log file 
Jun-27 17:04:21.420 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/bactmap -profile singularity
Jun-27 17:04:21.547 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 22.04.4
Jun-27 17:04:23.140 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/windell/.nextflow/assets/nf-core/bactmap/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/bactmap.git
Jun-27 17:04:23.161 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/windell/.nextflow/assets/nf-core/bactmap/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/bactmap.git
Jun-27 17:04:24.570 [main] DEBUG nextflow.config.ConfigBuilder - Found config home: /home/windell/.nextflow/config
Jun-27 17:04:24.570 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/windell/.nextflow/assets/nf-core/bactmap/nextflow.config
Jun-27 17:04:24.572 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /mnt/work/eresearch_bio/nextflow/nf-core/bactmap/testdata/run01/nextflow.config
Jun-27 17:04:24.573 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/windell/.nextflow/config
Jun-27 17:04:24.573 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/windell/.nextflow/assets/nf-core/bactmap/nextflow.config
Jun-27 17:04:24.573 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/work/eresearch_bio/nextflow/nf-core/bactmap/testdata/run01/nextflow.config
Jun-27 17:04:24.579 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Jun-27 17:04:24.671 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Jun-27 17:04:25.275 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Jun-27 17:04:25.291 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-27 17:04:25.292 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-27 17:04:25.295 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jun-27 17:04:25.312 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Jun-27 17:04:25.611 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Jun-27 17:04:25.652 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, genotoul, alice, mjolnir_globe, uppmax, abims, nihbiowulf, nu_genomics, oist, sahmri, mpcdf, leicester, lugh, vsc_ugent, sage, cambridge, unibe_ibu, vai, podman, czbiohub_aws, jax, cheaha, ccga_med, test, google, computerome, seg_globe, sanger, pasteur, test_full, eddie, azurebatch, bi, bigpurple, cedars, docker, gis, eva, utd_ganymede, charliecloud, fgcz, conda, singularity, icr_davros, munin, rosalind, prince, hasta, hebbe, cfc, utd_sysbio, uzh, debug, genouest, cbe, ebc, ccga_dx, crick, marvin, phoenix, biohpc_gen, shifter, awsbatch, uct_hpc, imperial, maestro, aws_tower, binac]
Jun-27 17:04:25.721 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Jun-27 17:04:25.722 [main] INFO  nextflow.cli.CmdRun - Launching `https://github.com/nf-core/bactmap` [peaceful_bhaskara] DSL2 - revision: e83f8c5f0e [master]
Jun-27 17:04:25.723 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/windell/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Jun-27 17:04:25.727 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-27 17:04:25.768 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-27 17:04:25.768 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-27 17:04:25.770 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jun-27 17:04:25.780 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jun-27 17:04:25.780 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.4.0
Jun-27 17:04:25.808 [main] INFO  org.pf4j.AbstractPluginManager - Plugin '[email protected]' resolved
Jun-27 17:04:25.808 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin '[email protected]'
Jun-27 17:04:26.133 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started [email protected]
Jun-27 17:04:26.278 [main] DEBUG nextflow.Session - Session uuid: 102eada9-1cd2-4eab-99eb-61fa2212febc
Jun-27 17:04:26.278 [main] DEBUG nextflow.Session - Run name: peaceful_bhaskara
Jun-27 17:04:26.279 [main] DEBUG nextflow.Session - Executor pool size: 2
Jun-27 17:04:26.293 [main] DEBUG nextflow.config.ConfigBuilder - Found config home: /home/windell/.nextflow/config
Jun-27 17:04:26.293 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/windell/.nextflow/assets/nf-core/bactmap/nextflow.config
Jun-27 17:04:26.293 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /mnt/work/eresearch_bio/nextflow/nf-core/bactmap/testdata/run01/nextflow.config
Jun-27 17:04:26.293 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/windell/.nextflow/config
Jun-27 17:04:26.293 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/windell/.nextflow/assets/nf-core/bactmap/nextflow.config
Jun-27 17:04:26.293 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/work/eresearch_bio/nextflow/nf-core/bactmap/testdata/run01/nextflow.config
Jun-27 17:04:26.294 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Jun-27 17:04:26.346 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Jun-27 17:04:26.779 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Jun-27 17:04:26.803 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, genotoul, alice, mjolnir_globe, uppmax, abims, nihbiowulf, nu_genomics, oist, sahmri, mpcdf, leicester, lugh, vsc_ugent, sage, cambridge, unibe_ibu, vai, podman, czbiohub_aws, jax, cheaha, ccga_med, test, google, computerome, seg_globe, sanger, pasteur, test_full, eddie, azurebatch, bi, bigpurple, cedars, docker, gis, eva, utd_ganymede, charliecloud, fgcz, conda, singularity, icr_davros, munin, rosalind, prince, hasta, hebbe, cfc, utd_sysbio, uzh, debug, genouest, cbe, ebc, ccga_dx, crick, marvin, phoenix, biohpc_gen, shifter, awsbatch, uct_hpc, imperial, maestro, aws_tower, binac]
Jun-27 17:04:26.852 [main] DEBUG nextflow.cli.CmdRun -
  Version: 22.04.4 build 5706
  Created: 19-06-2022 20:51 UTC (20-06-2022 06:51 AEDT)
  System: Linux 4.12.14-122.121-default
  Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.2+9
  Encoding: UTF-8 (UTF-8)
  Process: 7733@cl4n058 [10.13.1.8]
  CPUs: 2 - Mem: 377.2 GB (154.8 GB) - Swap: 2 GB (1.8 GB)
Jun-27 17:04:26.914 [main] DEBUG nextflow.Session - Work-dir: /mnt/work/eresearch_bio/nextflow/nf-core/bactmap/testdata/run01/work [nfs]
Jun-27 17:04:26.935 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-27 17:04:26.949 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-27 17:04:26.975 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Jun-27 17:04:27.491 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-27 17:04:27.513 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 3; maxThreads: 1000
Jun-27 17:04:27.782 [main] DEBUG nextflow.Session - Session start invoked
Jun-27 17:04:27.786 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /mnt/work/eresearch_bio/nextflow/nf-core/bactmap/testdata/run01/results/pipeline_info/execution_trace_2022-06-27_17-04-25.txt
Jun-27 17:04:27.875 [main] DEBUG io.seqera.tower.plugin.TowerClient - Creating Tower observer -- endpoint=https://nftower.qut.edu.au/api; requestInterval=1s; aliveInterval=1m; maxRetries=5; backOffBase=3; backOffDelay=250
Jun-27 17:04:27.997 [main] DEBUG nextflow.Session - Using default localLib path: /home/windell/.nextflow/assets/nf-core/bactmap/lib
Jun-27 17:04:28.008 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/windell/.nextflow/assets/nf-core/bactmap/lib
Jun-27 17:04:28.009 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/windell/.nextflow/assets/nf-core/bactmap/lib/nfcore_external_java_deps.jar
Jun-27 17:04:29.524 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-27 17:04:29.931 [main] INFO  nextflow.Nextflow -

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/bactmap v1.0.0
------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : peaceful_bhaskara
  containerEngine: singularity
  launchDir      : /mnt/work/eresearch_bio/nextflow/nf-core/bactmap/testdata/run01
  workDir        : /mnt/work/eresearch_bio/nextflow/nf-core/bactmap/testdata/run01/work
  projectDir     : /home/windell/.nextflow/assets/nf-core/bactmap
  userName       : windell
  profile        : singularity
  configFiles    : /home/windell/.nextflow/config, /home/windell/.nextflow/assets/nf-core/bactmap/nextflow.config, /mnt/work/eresearch_bio/nextflow/nf-core/bactmap/testdata/run01/nextflow.config

Input/output options
  input          : samplesheet.csv

Compulsory parameters
  reference      : NCTC13799.fna

Optional pipeline steps
  trim           : false
  adapter_file   : /home/windell/.nextflow/assets/nf-core/bactmap/assets/adapters.fas
  rapidnj        : true
  fasttree       : true
  iqtree         : true
  raxmlng        : true

Max job request options
  max_cpus       : 2
  max_memory     : 2.GB
  max_time       : 1.h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/bactmap for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/bactmap/blob/master/CITATIONS.md
------------------------------------------------------
Jun-27 17:04:35.850 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:35.850 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:35.860 [main] DEBUG nextflow.executor.Executor - [warm up] executor > pbspro
Jun-27 17:04:35.865 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'pbspro' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
Jun-27 17:04:35.869 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbspro' > queue-stat-interval: 1m
Jun-27 17:04:36.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_BACTMAP:BACTMAP:BWA_INDEX
Jun-27 17:04:36.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWA_INDEX` matches process NFCORE_BACTMAP:BACTMAP:BWA_INDEX
Jun-27 17:04:36.048 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.048 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.076 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_BACTMAP:BACTMAP:SUB_SAMPLING:MASH_SKETCH
Jun-27 17:04:36.078 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.078 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.107 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_BACTMAP:BACTMAP:SUB_SAMPLING:RASUSA
Jun-27 17:04:36.108 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.108 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.184 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_BACTMAP:BACTMAP:BWA_MEM
Jun-27 17:04:36.186 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.188 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.205 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_BACTMAP:BACTMAP:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT
Jun-27 17:04:36.205 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_SORT` matches process NFCORE_BACTMAP:BACTMAP:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT
Jun-27 17:04:36.206 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.206 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.214 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_BACTMAP:BACTMAP:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX
Jun-27 17:04:36.216 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.216 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.232 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_BACTMAP:BACTMAP:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Jun-27 17:04:36.233 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.234 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.250 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_BACTMAP:BACTMAP:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Jun-27 17:04:36.250 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.250 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.258 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_BACTMAP:BACTMAP:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Jun-27 17:04:36.261 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.261 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.278 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_BACTMAP:BACTMAP:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP
Jun-27 17:04:36.279 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.279 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.285 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_BACTMAP:BACTMAP:VARIANTS_BCFTOOLS:BCFTOOLS_FILTER
Jun-27 17:04:36.285 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.286 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.301 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_BACTMAP:BACTMAP:VCF2PSEUDOGENOME
Jun-27 17:04:36.303 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.303 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.320 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_BACTMAP:BACTMAP:ALIGNPSEUDOGENOMES
Jun-27 17:04:36.323 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.324 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.339 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_BACTMAP:BACTMAP:SNPSITES
Jun-27 17:04:36.341 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.341 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.351 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_BACTMAP:BACTMAP:CREATE_PHYLOGENY:RAPIDNJ
Jun-27 17:04:36.352 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.352 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.363 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_BACTMAP:BACTMAP:CREATE_PHYLOGENY:FASTTREE
Jun-27 17:04:36.363 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.363 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.373 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_BACTMAP:BACTMAP:CREATE_PHYLOGENY:IQTREE
Jun-27 17:04:36.374 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.374 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.379 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high,process_long` for process with name NFCORE_BACTMAP:BACTMAP:CREATE_PHYLOGENY:RAXMLNG
Jun-27 17:04:36.379 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_high,process_long` for process with name NFCORE_BACTMAP:BACTMAP:CREATE_PHYLOGENY:RAXMLNG
Jun-27 17:04:36.379 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.379 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.396 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbspro
Jun-27 17:04:36.396 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbspro'
Jun-27 17:04:36.469 [main] DEBUG nextflow.Session - Session aborted -- Cause: Access to 'FASTP.out' is undefined since the process 'FASTP' has not been invoked before accessing the output attribute
Jun-27 17:04:36.507 [main] DEBUG nextflow.Session - The following nodes are still active:
  [operator] splitCsv
  [operator] map
  [operator] map
  [operator] combine
  [operator] ifEmpty
  [operator] mix
  [operator] ifEmpty
  [operator] mix
  [operator] join
  [operator] ifEmpty
  [operator] mix
  [operator] ifEmpty
  [operator] mix
  [operator] map
  [operator] collect
  [operator] branch
  [operator] view
  [operator] map
  [operator] ifEmpty
  [operator] mix
  [operator] ifEmpty
  [operator] mix
  [operator] ifEmpty
  [operator] mix
  [operator] ifEmpty
  [operator] mix
  [operator] ifEmpty
  [operator] mix
  [operator] map
  [operator] collect
  [operator] collect
  [operator] ifEmpty
  [operator] collect
  [operator] collectFile

Jun-27 17:04:36.559 [main] ERROR nextflow.cli.Launcher - Access to 'FASTP.out' is undefined since the process 'FASTP' has not been invoked before accessing the output attribute
nextflow.exception.ScriptRuntimeException: Access to 'FASTP.out' is undefined since the process 'FASTP' has not been invoked before accessing the output attribute
        at nextflow.script.ProcessDef.getOut(ProcessDef.groovy:153)
        at jdk.internal.reflect.GeneratedMethodAccessor120.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.MethodMetaProperty$GetBeanMethodMetaProperty.getProperty(MethodMetaProperty.java:76)
        at org.codehaus.groovy.runtime.callsite.GetEffectivePogoPropertySite.getProperty(GetEffectivePogoPropertySite.java:85)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGetProperty(AbstractCallSite.java:329)
        at Script_c99ee09b$_runScript_closure1$_closure3.doCall(Script_c99ee09b:230)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at groovy.lang.Closure.call(Closure.java:406)
        at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205)
        at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189)
        at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:52)
        at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:41)
        at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:94)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:350)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176)
        at Script_14934cd2$_runScript_closure1$_closure3.doCall(Script_14934cd2:34)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at groovy.lang.Closure.call(Closure.java:406)
        at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205)
        at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189)
        at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:52)
        at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:41)
        at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:94)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:350)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176)
        at Script_14934cd2$_runScript_closure2$_closure4.doCall(Script_14934cd2:48)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at groovy.lang.Closure.call(Closure.java:406)
        at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205)
        at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189)
        at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:52)
        at nextflow.script.ChainableDef$invoke_a.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
        at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:208)
        at nextflow.script.BaseScript.run(BaseScript.groovy:217)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:220)
        at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:212)
        at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:120)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:337)
        at nextflow.cli.Launcher.run(Launcher.groovy:480)
        at nextflow.cli.Launcher.main(Launcher.groovy:639)
Jun-27 17:04:36.601 [Actor Thread 6] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null

System

  • Hardware: HPC
  • Executor: PBSPRO
  • OS: SUSE
  • Version 12

Nextflow Installation

  • Version: 22.04.4

Container engine

  • Engine: singularity
  • version: 3.9.8-1
@craigwindell craigwindell added the bug Something isn't working label Jun 27, 2022
@adamd3
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adamd3 commented Mar 20, 2023 •
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I got the same error. It is caused by the MULTIQC process attempting to access the output from FASTP (which has not been run because trimming was off).

The MULTIQC process cannot currently be switched off (even when --skip_multiqc true is provided).

A simple fix would be to turn off MultiQC when trimming is disabled, or to run it without the FASTP output.

@adamd3 adamd3 mentioned this issue Mar 20, 2023
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@jacquikeane
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I am experiencing the same issue. Any plans to add a fix to allow the pipeline to be run without the trimming/fastp step?

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@jacquikeane @adamd3 @craigwindell