Error in file braker.pl at line 5404. Failed to execute gmes_petap.pl

[natt1621]

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.

[Somnous1998]

Hello, have you solved this problem in the back? I was in the same situation as you after successfully completing three genome annotations.

Wed May 1 21:04:42 2024: Log information is stored in file /datapool/home/yangzc/soft/pacbio/gapfiller-main/MEGAHIT_JYEX1/braker3/braker/braker.log

ERROR in file /datapool/home/yangzc/soft/pacbio/BRAKER-3.0.8/scripts/braker.pl at line 5414 Failed to execute: /datapool/home/yangzc/miniconda3/envs/Augustus/bin/perl /datapool/home/yangzc/soft/pacbio/GeneMark-ETP/bin/gmes/gmes_petap.pl --verbose --seq /datapool/home/yangzc/soft/pacbio/gapfiller-main/MEGAHIT_JYEX1/braker3/braker/genome.fa --EP /datapool/home/yangzc/soft/pacbio/gapfiller-main/MEGAHIT_JYEX1/braker3/braker/genemark_hintsfile.gff --cores=1 --gc_donor 0.001 --evidence /datapool/home/yangzc/soft/pacbio/gapfiller-main/MEGAHIT_JYEX1/braker3/braker/genemark_evidence.gff --soft_mask auto 1>/datapool/home/yangzc/soft/pacbio/gapfiller-main/MEGAHIT_JYEX1/braker3/braker/GeneMark-EP.stdout 2>/datapool/home/yangzc/soft/pacbio/gapfiller-main/MEGAHIT_JYEX1/braker3/braker/errors/GeneMark-EP.stderr Failed to execute: /datapool/home/yangzc/miniconda3/envs/Augustus/bin/perl /datapool/home/yangzc/soft/pacbio/GeneMark-ETP/bin/gmes/gmes_petap.pl --verbose --seq /datapool/home/yangzc/soft/pacbio/gapfiller-main/MEGAHIT_JYEX1/braker3/braker/genome.fa --EP /datapool/home/yangzc/soft/pacbio/gapfiller-main/MEGAHIT_JYEX1/braker3/braker/genemark_hintsfile.gff --cores=1 --gc_donor 0.001 --evidence /datapool/home/yangzc/soft/pacbio/gapfiller-main/MEGAHIT_JYEX1/braker3/braker/genemark_evidence.gff --soft_mask auto 1>/datapool/home/yangzc/soft/pacbio/gapfiller-main/MEGAHIT_JYEX1/braker3/braker/GeneMark-EP.stdout 2>/datapool/home/yangzc/soft/pacbio/gapfiller-main/MEGAHIT_JYEX1/braker3/braker/errors/GeneMark-EP.stderr !

Do you have any suggestions? Thank you very much for your help!