error :get_gc_content.py

[cpouchon]

Hi,

I am trying to use BRAKER to annotate genomes using protein sequences.

I have followed the instructions to create a Docker image for BRAKER. However, when I attempt to run BRAKER, I encounter the following issue:

#**********************************************************************************
#                               BRAKER CONFIGURATION                               
#**********************************************************************************
# BRAKER CALL: /opt/BRAKER/scripts/braker.pl --genome=/home/users/p/pouchon/Alismatales/kit/genomes/Amorphophallus_konjac_78372_GCA_022559845.fa --prot_seq=/home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/prots_for_annot.faa --workingdir=test4 --GENEMARK_PATH=/gmes
# Fri Nov 29 16:47:25 2024: braker.pl version 3.0.8
# Fri Nov 29 16:47:25 2024: Creating directory /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4.
# Fri Nov 29 16:47:25 2024: Only Protein input detected, BRAKER will be executed in EP mode (BRAKER2).
# Fri Nov 29 16:47:25 2024: Configuring of BRAKER for using external tools...
# Fri Nov 29 16:47:25 2024: Trying to set $AUGUSTUS_CONFIG_PATH...
# Fri Nov 29 16:47:25 2024: Found environment variable $AUGUSTUS_CONFIG_PATH.
# Fri Nov 29 16:47:25 2024: Checking /opt/Augustus/config/ as potential path for $AUGUSTUS_CONFIG_PATH.
# Fri Nov 29 16:47:25 2024: Success! Setting $AUGUSTUS_CONFIG_PATH to /opt/Augustus/config/!
# Fri Nov 29 16:47:25 2024: Trying to set $AUGUSTUS_BIN_PATH...
# Fri Nov 29 16:47:25 2024: Found environment variable $AUGUSTUS_BIN_PATH.
# Fri Nov 29 16:47:25 2024: Checking /opt/Augustus/bin/ as potential path for $AUGUSTUS_BIN_PATH.
# Fri Nov 29 16:47:25 2024: Success! Setting $AUGUSTUS_BIN_PATH to /opt/Augustus/bin/!
# Fri Nov 29 16:47:25 2024: Trying to set $AUGUSTUS_SCRIPTS_PATH...
# Fri Nov 29 16:47:25 2024: Found environment variable $AUGUSTUS_SCRIPTS_PATH.
# Fri Nov 29 16:47:25 2024: Checking /opt/Augustus/scripts/ as potential path for $AUGUSTUS_SCRIPTS_PATH.
# Fri Nov 29 16:47:25 2024: Success! Setting $AUGUSTUS_SCRIPTS_PATH to /opt/Augustus/scripts/!
# Fri Nov 29 16:47:25 2024: Trying to set $PYTHON3_PATH...
# Fri Nov 29 16:47:25 2024: Did not find environment variable $PYTHON3_PATH.
# Fri Nov 29 16:47:25 2024: Trying to guess PYTHON3_PATH from location of python3 executable that is available in your $PATH
# Fri Nov 29 16:47:25 2024: Checking /opt/conda/bin as potential path for $PYTHON3_PATH.
# Fri Nov 29 16:47:25 2024: Success! Setting $PYTHON3_PATH to /opt/conda/bin!
# Fri Nov 29 16:47:25 2024: Trying to set $GENEMARK_PATH...
# Fri Nov 29 16:47:25 2024: Found command line argument $GENEMARK_PATH.
# Fri Nov 29 16:47:25 2024: Checking /gmes as potential path for $GENEMARK_PATH.
#*********
# WARNING: /gmes is not a directory. Will not set $GENEMARK_PATH to /gmes!
#*********
# Fri Nov 29 16:47:25 2024: Found environment variable $GENEMARK_PATH.
# Fri Nov 29 16:47:25 2024: Checking /opt/ETP/bin as potential path for $GENEMARK_PATH.
#*********
# WARNING: Couldn't find gmes_petap.pl in /opt/ETP/bin. Will not set $GENEMARK_PATH to /opt/ETP/bin!
#*********
# Fri Nov 29 16:47:25 2024: Trying to guess GENEMARK_PATH from location of gmes_petap.pl executable that is available in your $PATH
# Fri Nov 29 16:47:25 2024: Checking /opt/ETP/bin/gmes as potential path for $GENEMARK_PATH.
# Fri Nov 29 16:47:25 2024: Success! Setting $GENEMARK_PATH to /opt/ETP/bin/gmes!
# Fri Nov 29 16:47:25 2024: Trying to set $DIAMOND_PATH...
# Fri Nov 29 16:47:25 2024: Did not find environment variable $DIAMOND_PATH.
# Fri Nov 29 16:47:25 2024: Trying to guess DIAMOND_PATH from location of diamond executable that is available in your $PATH
# Fri Nov 29 16:47:25 2024: Checking /opt/ETP/tools as potential path for $DIAMOND_PATH.
# Fri Nov 29 16:47:25 2024: Success! Setting $DIAMOND_PATH to /opt/ETP/tools!
# Fri Nov 29 16:47:25 2024: Trying to set $PROTHINT_PATH...
# Fri Nov 29 16:47:25 2024: Did not find environment variable $PROTHINT_PATH.
# Fri Nov 29 16:47:25 2024: Trying to guess PROTHINT_PATH from location of prothint.py executable that is available in your $PATH
# Fri Nov 29 16:47:25 2024: Checking /opt/ETP/bin/gmes/ProtHint/bin as potential path for $PROTHINT_PATH.
# Fri Nov 29 16:47:25 2024: Success! Setting $PROTHINT_PATH to /opt/ETP/bin/gmes/ProtHint/bin!
# Fri Nov 29 16:47:25 2024: Trying to set $TSEBRA_PATH...
# Fri Nov 29 16:47:25 2024: Did not find environment variable $TSEBRA_PATH.
# Fri Nov 29 16:47:25 2024: Trying to guess TSEBRA_PATH from location of tsebra.py executable that is available in your $PATH
# Fri Nov 29 16:47:25 2024: Checking /opt/TSEBRA/bin as potential path for $TSEBRA_PATH.
# Fri Nov 29 16:47:25 2024: Success! Setting $TSEBRA_PATH to /opt/TSEBRA/bin!
# Fri Nov 29 16:47:25 2024: Trying to set $CDBTOOLS_PATH...
# Fri Nov 29 16:47:25 2024: Did not find environment variable $CDBTOOLS_PATH.
# Fri Nov 29 16:47:25 2024: Trying to guess CDBTOOLS_PATH from location of cdbfasta executable that is available in your $PATH
# Fri Nov 29 16:47:25 2024: Checking /opt/cdbfasta as potential path for $CDBTOOLS_PATH.
# Fri Nov 29 16:47:25 2024: Success! Setting $CDBTOOLS_PATH to /opt/cdbfasta!
# Fri Nov 29 16:47:25 2024: BRAKER will execute GeneMark-EP for training GeneMark and generating a training gene set for AUGUSTUS, using protein information as sole extrinsic evidence source.
#*********
# IMPORTANT INFORMATION: no species for identifying the AUGUSTUS  parameter set that will arise from this BRAKER run was set. BRAKER will create an AUGUSTUS parameter set with name Sp_1. This parameter set can be used for future BRAKER/AUGUSTUS prediction runs for the same species. It is usually not necessary to retrain AUGUSTUS with novel extrinsic data if a high quality parameter set already exists.
#*********
#**********************************************************************************
#                               CREATING DIRECTORY STRUCTURE                       
#**********************************************************************************
# Fri Nov 29 16:47:25 2024: creating file that contains citations for this BRAKER run at /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4/what-to-cite.txt...
# Fri Nov 29 16:47:25 2024: create working directory /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4/GeneMark-EP.
mkdir /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4/GeneMark-EP
# Fri Nov 29 16:47:25 2024: create working directory /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4/GeneMark-ES.
mkdir /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4/GeneMark-ES
# Fri Nov 29 16:47:25 2024: create working directory /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4/species
mkdir /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4/species
# Fri Nov 29 16:47:25 2024: create working directory /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4/errors
mkdir /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4/errors
# Fri Nov 29 16:47:26 2024: changing into working directory /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4
cd /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4
# Fri Nov 29 16:47:26 2024: getting GC content of the genome
/opt/BRAKER/scripts/get_gc_content.py --sequences /home/users/p/pouchon/Alismatales/kit/genomes/Amorphophallus_konjac_78372_GCA_022559845.fa --print_sequence_length 1> /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4/gc_content.out 2> /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/test4/errors/gc_content.stderr

ERROR in file /opt/BRAKER/scripts/braker.pl at line 5942
failed to execute: /opt/BRAKER/scripts/get_gc_content.py --sequences /home/users/p/pouchon/Alismatales/kit/genomes/Amorphophallus_konjac_78372_GCA_022559845.fa --print_sequence_length 1> /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/braker/gc_content.out 2> /home/users/p/pouchon/Alismatales/kit/annotations_for_genomes/braker/errors/gc_content.stderr!

Could you please advise on how to resolve this issue?

Thanks a lot for your help!

Cheers,

Charles

[bijendrabio]

@cpouchon Check this: #743