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Error reading fasta sequences - please check input files! #14

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kashiff007 opened this issue Jun 16, 2022 · 3 comments
Open

Error reading fasta sequences - please check input files! #14

kashiff007 opened this issue Jun 16, 2022 · 3 comments

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@kashiff007
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kashiff007 commented Jun 16, 2022 •
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Hi thanks for this great software. While using this I am unable to start with the continuous error of "Error reading fasta sequences - please check input files!". This error also occurring with test-seqs.fas.

Full log output pasted below:

python2.7 ~/Software/flexidot/code/flexidot_v1.00.py -i ~/Software/flexidot/test-data/test-seqs.fas -g ~/Software/flexidot/test-data/example2.gff3 -G ~/Software/flexidot/test-data/gff_color.config -o Cluster_94644.txt.bed.pdf -p 2
Installing Python module: colour
	python -m pip install colour

Requirement already satisfied: colour in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (0.1.5)


Please install module colour manually
Installing Python module: colormap
	python -m pip install colormap

Installing Python module: easydev
	python -m pip install easydev

Requirement already satisfied: colormap in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (1.0.4)
Requirement already satisfied: easydev in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (0.12.0)
Requirement already satisfied: colorama in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from easydev) (0.4.4)
Requirement already satisfied: pexpect in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from easydev) (4.8.0)
Requirement already satisfied: colorlog in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from easydev) (6.6.0)
Requirement already satisfied: ptyprocess>=0.5 in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from pexpect->easydev) (0.7.0)


Please install module colormap manually
Installing Python module: biopython
	python -m pip install biopython

Requirement already satisfied: biopython in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (1.79)
Requirement already satisfied: numpy in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from biopython) (1.21.5)


Please install module biopython manually
Installing Python module: regex
	python -m pip install regex

Requirement already satisfied: regex in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (2022.3.15)


Please install module regex manually

...reading input arguments...
fasta file #1: /Users/nawazk/Software/flexidot/test-data/test-seqs.fas
GFF file #1: /Users/nawazk/Software/flexidot/test-data/example2.gff3

----------------------------------------------------------------------

INPUT/OUTPUT OPTIONS...

Input fasta file:                                  /Users/nawazk/Software/flexidot/test-data/test-seqs.fas
Automatic fasta collection from current directory: False
Collage output:                                    True
Number of columns per page:                        4
Number of rows per page:                           5
File format:                                       png
Residue type is nucleotide:                        True


CALCULATION PARAMETERS...

Wordsize:                                          7
Plotting mode:                                     2
                                                   all-against-all 
Ambiguity handling:                                False
Reverse complement scanning:                       True
Alphabetic sorting:                                False
Prefix for output files:                           Cluster_94644.txt.bed.pdf


LCS SHADING OPTIONS (plotting_mode 'all-against-all' only)...

LCS shading:                                       False
LCS shading interval number:                       5
LCS shading reference:                             maximal LCS length
LCS shading orientation:                           forward


GRAPHIC FORMATTING...

Plot size:                                         10
Line width:                                        1
Line color:                                        black
Reverse line color:                                #009243
X label position:                                  True
Label size:                                        10
Spacing:                                           0.04
Title length (limit number of characters):         inf
Length scaling:                                    False
----------------------------------------------------------------------


==================================================

Reading GFF color configuration file
----------------------------

=> /Users/nawazk/Software/flexidot/test-data/gff_color.config

Updating GFF color configuration with custom specifications

1 feature type specifications overwritten:
	repeat_region

GFF color specification updated acc. to /Users/nawazk/Software/flexidot/test-data/gff_color.config
	misc_feat, misc_feature, spacer3, spacer2, spacer1, cds, misc, ltr_retrotransposon, ppt, tandem_repeat, target_site_duplication, intron, spacerzoom, repeat, ltr-retro, long_terminal_repeat, exon, others, orf, transposable_element, ltr, pbs, repeat_region, utr, repeat_region_rev, orf_rev, gene


==================================================

Running plotting modes 2
Error reading fasta sequences - please check input files!

Failed to load sequences

	 0.000445127487183 seconds

No image files were created!

==================================================

##################################################
##################################################

Thank you for using FlexiDot!

```
@molbio-dresden
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molbio-dresden commented Jun 16, 2022 via email

@kashiff007
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Dear Tony,

Thank you very much.

Best,
Kashif

@NAalytics
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Hello all- I am having similar issues. While the program is giving errors in a python=3.6 environment, in an environment where python=2.7 all other packages (eg, color, like it was shown above) give errors. I am unable to run the program in both of these environments. If a solution is available, please let me know.
With best wishes.
Massa

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@kashiff007 @molbio-dresden @NAalytics