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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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When running BRAKER3 using Singularity, an error occurred #825

Closed 1039931841 closed 1 month ago

1039931841 commented 1 month ago

The steps I followed to use Singularity are as follows: singularity build braker3.sif docker://teambraker/braker3:latest

export BRAKER_SIF=/ME4012_Vol0002/Ahome_Dir/liming/braker3/braker3.sif

singularity instance start braker3.sif braker3

singularity shell braker3.sif

nohup sh zj_new.sh

The content of zj_new.sh is as follows:

#########################################################################
# File Name: zj_new.sh
# Author: liming
# mail: 1039931841@qq.com
# Created Time: Mon 13 May 2024 09:20:42 AM CST
#########################################################################
#!/bin/bash
braker.pl --genome=/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/03-RepeatMask-softmasking/RepeatMasker/purged.FINAL.fasta.masked --prot_seq=/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/db_pep.fasta --gff3 --workingdir=/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker --threads 48 --bam=/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/control_1.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/control_2.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/control_3.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/control_4.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/FL.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/ML.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/T20210624_00036.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/T20210624_00037.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/T20210624_00038.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/T20210624_00043.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/T20210624_00044.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/T20210624_00051.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/T20210624_00052.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/T20210624_00053.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/T20210624_00057.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/T20210624_00058.bam,/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/mapping/T20210624_00059.bam

Midway through the process, I encountered the following error:

# Tue May 14 10:12:53 2024: Log information is stored in file /ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/braker.log
ERROR in file /opt/BRAKER/scripts/braker.pl at line 6288
Failed to execute: /opt/Augustus/bin//etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/ME4012_Vol0002/Ahome_Dir/liming/.augustus /ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/train.f.gb 1> /ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/gbFilterEtraining.stdout 2>/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/errors/gbFilterEtraining.stderr

Then I checked the gbFilterEtraining.stderr file, but I found that the file was empty. I also checked the braker.log file, and it stopped at the following point:

# Tue May 14 16:54:11 2024: Filtering train.gb for "good" mRNAs:
/usr/bin/perl /opt/Augustus/scripts/filterGenesIn_mRNAname.pl /ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/traingenes.gtf /ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/train.gb > /ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/train.f.gb 2>/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/errors/filterGenesIn_mRNAname.stderr
# Tue May 14 16:54:15 2024: Genbank format file /ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/train.f.gb contains 10114 genes.
# Tue May 14 16:54:15 2024: Running etraining to catch gene structure inconsistencies:
/opt/Augustus/bin//etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/ME4012_Vol0002/Ahome_Dir/liming/.augustus /ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/train.f.gb 1> /ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/gbFilterEtraining.stdout 2>/ME4012_Vol0002/Ahome_Dir/liming/zj_assembly/14.Structural_and_functional_annotations_ZJ_genomic/04-braker/errors/gbFilterEtraining.stderr

In addition, I have also uploaded my running logs, nohup.out.txt and braker.log.Could you please take a look and let me know how can I solve this problem. Thank you very much. Any suggestions you have are crucial to me.

braker.log

nohup.out.txt