molbio-dresden
commented
2 years ago Dear Mr. Nawaz,
I will have a look, likely over the weekend!
Best wishes
Tony
Dr. Tony Heitkam Technische Universität Dresden Faculty of Biology Zellescher Weg 20b | Room E35 | D-01062 Dresden
Tel: (+49) 0351 463 39593 Email: @.***
Von: Kashif Nawaz @.***> Gesendet: Donnerstag, 16. Juni 2022 11:47:05 An: molbio-dresden/flexidot Cc: Subscribed Betreff: [molbio-dresden/flexidot] Error reading fasta sequences - please check input files! (Issue #14)
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 #1https://github.com/molbio-dresden/flexidot/issues/1: /Users/nawazk/Software/flexidot/test-data/test-seqs.fas GFF file #1https://github.com/molbio-dresden/flexidot/issues/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!
`
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kashiff007
NAalytics
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: