Error in file braker.pl at line 5404. Failed to execute gmes_petap.pl
0
0
Entering edit mode
8 weeks ago
natt1621 • 0

Hi, I'm trying to run Braker to predict genes, but I'm getting this error with gmes_petap.pl script. When I try to look out on 'errors' folder and GeneMark-EP.stderr file is empty, so I can't find what's really happening or how to fix it.

I use the following command/syntax to run braker:

braker.pl --genome=a_fraterculus_s.fasta --hints=prothint_augustus.gff --species=anastrepha --threads=12
#**********************************************************************************
#                               BRAKER CONFIGURATION                               
#**********************************************************************************
# BRAKER CALL: /home/natalia/Programas/BRAKER-master/scripts/braker.pl --genome=a_fraterculus_s.fasta --hints=prothint_augustus.gff --species=anastrepha --threads=12
# Wed Feb 21 16:20:46 2024: braker.pl version 3.0.7
# Wed Feb 21 16:20:46 2024: Checking whether hints from RNA-Seq and/or proteins are present in hintsfile
# Wed Feb 21 16:20:46 2024: Only Protein input detected, BRAKER will be executed in EP mode (BRAKER2).
# Wed Feb 21 16:20:46 2024: Configuring of BRAKER for using external tools...
# Wed Feb 21 16:20:46 2024: Trying to set $AUGUSTUS_CONFIG_PATH...
# Wed Feb 21 16:20:46 2024: Did not find environment variable $AUGUSTUS_CONFIG_PATH.
# Wed Feb 21 16:20:46 2024: Checking /usr/bin/../config as potential path for $AUGUSTUS_CONFIG_PATH.
#*********
# WARNING: /usr/bin/../config is not a directory. Will not set $AUGUSTUS_CONFIG_PATH to /usr/bin/../config!
#*********
# Wed Feb 21 16:20:46 2024: Checking /usr/share/augustus/config as potential path for $AUGUSTUS_CONFIG_PATH.
# Wed Feb 21 16:20:46 2024: Success! Setting $AUGUSTUS_CONFIG_PATH to /usr/share/augustus/config!
# Wed Feb 21 16:20:46 2024: WARNING: in file /home/natalia/Programas/BRAKER-master/scripts/braker.pl at line 1931
AUGUSTUS_CONFIG_PATH/species (in this case /usr/share/augustus/config/species) is not writeable. BRAKER will try to copy the AUGUSTUS config directory to a writeable location.
# Wed Feb 21 16:20:46 2024: Log information is stored in file /home/natalia/Documentos/prueba2_braker/braker/braker.log
#*********
# WARNING: in file /home/natalia/Programas/BRAKER-master/scripts/braker.pl at line 1411
file /home/natalia/Documentos/prueba2_braker/braker/genome.fa contains a highly fragmented assembly (689787 scaffolds). This may lead to problems when running AUGUSTUS via braker in parallelized mode. You set --threads=12. You should run braker.pl in linear mode on such genomes, though (--threads=1).
#*********
#*********
# WARNING: 
# The hints file(s) for GeneMark-EX contain less than 1000 introns. (In total, 407 unique introns are contained.)
# Genemark-EX might fail due to the low number of hints.
#*********
ERROR in file /home/natalia/Programas/BRAKER-master/scripts/braker.pl at line 5404
Failed to execute: /usr/bin/perl /home/natalia/Programas/GeneMark-ETP/bin/gmes/gmes_petap.pl --verbose --seq /home/natalia/Documentos/prueba2_braker/braker/genome.fa --EP /home/natalia/Documentos/prueba2_braker/braker/genemark_hintsfile.gff --cores=12  --gc_donor 0.001 --evidence /home/natalia/Documentos/prueba2_braker/braker/genemark_evidence.gff  --soft_mask auto 1>/home/natalia/Documentos/prueba2_braker/braker/GeneMark-EP.stdout 2>/home/natalia/Documentos/prueba2_braker/braker/errors/GeneMark-EP.stderr
Failed to execute: /usr/bin/perl /home/natalia/Programas/GeneMark-ETP/bin/gmes/gmes_petap.pl --verbose --seq /home/natalia/Documentos/prueba2_braker/braker/genome.fa --EP /home/natalia/Documentos/prueba2_braker/braker/genemark_hintsfile.gff --cores=12  --gc_donor 0.001 --evidence /home/natalia/Documentos/prueba2_braker/braker/genemark_evidence.gff  --soft_mask auto 1>/home/natalia/Documentos/prueba2_braker/braker/GeneMark-EP.stdout 2>/home/natalia/Documentos/prueba2_braker/braker/errors/GeneMark-EP.stderr !

I don't know if the last warning of GeneMark-EX about introns interfere with this. I'm kind of new in this predicting genes thing, so any help would be appreciated. Thanks in advance.

perl braker • 225 views
ADD COMMENT

Login before adding your answer.

Traffic: 1842 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6