BRAKER
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Gaius-Augustus
Error on running test1.sh
I ran test1.sh in the example and got core dumped.
>cat test1.log
# Fri Jul 29 10:58:50 2022: Log information is stored in file /ddn/work/cjh/test/braker-2.1.6/tests/test1/braker.log
sh: line 1: 126276 Segmentation fault (core dumped) /app/redhat6/augustus/augustus-3.4.0/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-3.4.0/config /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.f.gb > /ddn/work/cjh/test/braker-2.1.6/tests/test1/gbFilterEtraining.stdout 2> /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/gbFilterEtraining.stderr
ERROR in file /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/braker.pl at line 7468
Failed to execute: /app/redhat6/augustus/augustus-3.4.0/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-3.4.0/config /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.f.gb 1> /ddn/work/cjh/test/braker-2.1.6/tests/test1/gbFilterEtraining.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/gbFilterEtraining.stderr
real 73m2.617s
user 20m38.514s
sys 295m9.583s
>cat test1/braker.log
#**********************************************************************************
# BRAKER CONFIGURATION
#**********************************************************************************
# BRAKER CALL: /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/braker.pl --genome=../genome.fa --bam=../RNAseq.bam --softmasking --workingdir=test1 --cores 8 --gm_max_intergenic 10000
# Fri Jul 29 10:58:49 2022: braker.pl version 2.1.6
# Fri Jul 29 10:58:49 2022: Creating directory /ddn/work/cjh/test/braker-2.1.6/tests/test1.
# Fri Jul 29 10:58:49 2022: Configuring of BRAKER for using external tools...
# Fri Jul 29 10:58:49 2022: Found environment variable $AUGUSTUS_CONFIG_PATH. Setting $AUGUSTUS_CONFIG_PATH to /app/redhat6/augustus/augustus-3.4.0/config
# Fri Jul 29 10:58:49 2022: Found environment variable $AUGUSTUS_BIN_PATH. Setting $AUGUSTUS_BIN_PATH to /app/redhat6/augustus/augustus-3.4.0/bin
# Fri Jul 29 10:58:49 2022: Found environment variable $AUGUSTUS_SCRIPTS_PATH. Setting $AUGUSTUS_SCRIPTS_PATH to /app/redhat6/augustus/augustus-3.4.0/scripts
# Fri Jul 29 10:58:49 2022: Found environment variable $PYTHON3_PATH. Setting $PYTHON3_PATH to /app/redhat6/anaconda3/bin
# Fri Jul 29 10:58:49 2022: Found environment variable $GENEMARK_PATH. Setting $GENEMARK_PATH to /app/redhat6/gmes/GeneMark-4.64_lic
# Fri Jul 29 10:58:49 2022: Found environment variable $BAMTOOLS_PATH. Setting $BAMTOOLS_PATH to /app/redhat6/bamtools/bamtools-2.5.1/bin
# Fri Jul 29 10:58:49 2022: Found environment variable $SAMTOOLS_PATH. Setting $SAMTOOLS_PATH to /app/redhat6/samtools/samtools-1.14/bin
# Fri Jul 29 10:58:49 2022: Found environment variable $DIAMOND_PATH. Setting $DIAMOND_PATH to /app/redhat6/diamond/diamond-0.9.24
# Fri Jul 29 10:58:49 2022: Found environment variable $CDBTOOLS_PATH. Setting $CDBTOOLS_PATH to /app/redhat6/cdbfasta/cdbfasta-1.00
#*********
# 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 Jul 29 10:58:50 2022: creating file that contains citations for this BRAKER run at /ddn/work/cjh/test/braker-2.1.6/tests/test1/what-to-cite.txt...
# Fri Jul 29 10:58:50 2022: create working directory /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET.
mkdir /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET
# Fri Jul 29 10:58:50 2022: create working directory /ddn/work/cjh/test/braker-2.1.6/tests/test1/species
mkdir /ddn/work/cjh/test/braker-2.1.6/tests/test1/species
# Fri Jul 29 10:58:50 2022: create working directory /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors
mkdir /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors
# Fri Jul 29 10:58:50 2022: changing into working directory /ddn/work/cjh/test/braker-2.1.6/tests/test1
cd /ddn/work/cjh/test/braker-2.1.6/tests/test1
# Fri Jul 29 10:58:50 2022: Creating parameter template files for AUGUSTUS with new_species.pl
# Fri Jul 29 10:58:50 2022: new_species.pl will create parameter files for species Sp_1 in /app/redhat6/augustus/augustus-3.4.0/config/species/Sp_1
perl /app/redhat6/augustus/augustus-3.4.0/scripts/new_species.pl --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-3.4.0/config 1> /dev/null 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/new_species.stderr
# Fri Jul 29 10:58:50 2022: check_fasta_headers(): Checking fasta headers of file /ddn/work/cjh/test/braker-2.1.6/tests/../genome.fa
#**********************************************************************************
# PROCESSING HINTS
#**********************************************************************************
# Fri Jul 29 10:58:50 2022: Converting bam files to hints
# Fri Jul 29 10:58:50 2022: Checking bam headers
# Fri Jul 29 10:58:50 2022: create header file /ddn/work/cjh/test/braker-2.1.6/tests/test1/RNAseq_header.sam
/app/redhat6/bamtools/bamtools-2.5.1/bin/bamtools header -in /ddn/work/cjh/test/braker-2.1.6/tests/../RNAseq.bam > /ddn/work/cjh/test/braker-2.1.6/tests/test1/RNAseq_header.sam
# Fri Jul 29 10:58:50 2022: Deleting SAM header file /ddn/work/cjh/test/braker-2.1.6/tests/test1/RNAseq_header.sam (will not be needed from here on)
# Fri Jul 29 10:58:50 2022: Deleting /ddn/work/cjh/test/braker-2.1.6/tests/test1/RNAseq_new_header.sam
# Fri Jul 29 10:58:50 2022: make hints from BAM file /ddn/work/cjh/test/braker-2.1.6/tests/../RNAseq.bam
/app/redhat6/augustus/augustus-3.4.0/bin/bam2hints --intronsonly --in=/ddn/work/cjh/test/braker-2.1.6/tests/../RNAseq.bam --out=/ddn/work/cjh/test/braker-2.1.6/tests/test1/bam2hints.temp.0.gff 1> /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/bam2hints.0.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/bam2hints.0.stderr
# Fri Jul 29 10:59:05 2022: add hints from BAM file /ddn/work/cjh/test/braker-2.1.6/tests/../RNAseq.bam to hints file
cat /ddn/work/cjh/test/braker-2.1.6/tests/test1/bam2hints.temp.0.gff >>/ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.temp.gff
# Fri Jul 29 10:59:05 2022: Checking for hints of src=C and with grp tags that should not be joined according to multiplicity
# Fri Jul 29 10:59:05 2022: Joining hints that are identical (& from the same source) into multiplicity hints (input file /ddn/work/cjh/test/braker-2.1.6/tests/test1/tmp_merge_hints.gff)
# Fri Jul 29 10:59:05 2022: sort hints of type rnaseq
cat /ddn/work/cjh/test/braker-2.1.6/tests/test1/tmp_merge_hints.gff | sort -n -k 4,4 | sort -s -n -k 5,5 | sort -s -n -k 3,3 | sort -s -k 1,1 >/ddn/work/cjh/test/braker-2.1.6/tests/test1/hints.rnaseq.temp.sort.gff
# Fri Jul 29 10:59:05 2022: join multiple hints
perl /app/redhat6/augustus/augustus-3.4.0/scripts/join_mult_hints.pl </ddn/work/cjh/test/braker-2.1.6/tests/test1/hints.rnaseq.temp.sort.gff >/ddn/work/cjh/test/braker-2.1.6/tests/test1/tmp_merge_hints.gff 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/join_mult_hints.rnaseq.stderr
mv /ddn/work/cjh/test/braker-2.1.6/tests/test1/tmp_merge_hints.gff /ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.temp.gff
# Fri Jul 29 10:59:06 2022: filter introns, find strand and change score to 'mult' entry
perl /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/filterIntronsFindStrand.pl /ddn/work/cjh/test/braker-2.1.6/tests/test1/genome.fa /ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.temp.gff --score 1>>/ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.gff 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/filterIntronsFindStrand.stderr
# Fri Jul 29 10:59:06 2022: rm /ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.temp.gff
# Fri Jul 29 10:59:06 2022: Preparing hints for running GeneMark
# Fri Jul 29 10:59:06 2022: Filtering intron hints for GeneMark from /ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.gff...
cat /ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff.rnaseq | sort -n -k 4,4 | sort -s -n -k 5,5 | sort -s -k 3,3 | sort -s -k 1,1 | /app/redhat6/augustus/augustus-3.4.0/scripts/join_mult_hints.pl > /ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff.rnaseq.tmp
mv /ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff.rnaseq.tmp /ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff
#**********************************************************************************
# RUNNING GENEMARK-EX
#**********************************************************************************
# Fri Jul 29 11:02:27 2022: Checking whether file /ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff contains enough hints and sufficient multiplicity information...
# Fri Jul 29 11:02:27 2022: Executing GeneMark-ET
# Fri Jul 29 11:02:27 2022: changing into GeneMark-ET directory /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET
cd /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET
# Fri Jul 29 11:02:27 2022: Executing gmes_petap.pl
perl /app/redhat6/gmes/GeneMark-4.64_lic/gmes_petap.pl --verbose --sequence=/ddn/work/cjh/test/braker-2.1.6/tests/test1/genome.fa --ET=/ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff --cores=8 --gc_donor 0.001 --soft_mask auto --max_intergenic=10000 1>/ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/GeneMark-ET.stderr
# Fri Jul 29 12:11:46 2022: change to working directory /ddn/work/cjh/test/braker-2.1.6/tests/test1
cd /ddn/work/cjh/test/braker-2.1.6/tests/test1
# Fri Jul 29 12:11:46 2022: Filtering output of GeneMark for generating training genes for AUGUSTUS
# Fri Jul 29 12:11:46 2022: Checking whether hintsfile contains single exon CDSpart hints or start/stop hints
# Fri Jul 29 12:11:46 2022: sorting GeneMark predictions in /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf
/app/redhat6/anaconda3/bin/python3 /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/sortGeneMark.py /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf > /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf.sorted 2> /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/sortGeneMark.err
mv /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf.sorted /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf
# Fri Jul 29 12:11:47 2022: filtering GeneMark genes by intron hints
perl /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/filterGenemark.pl --genemark=/ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf --hints=/ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.gff --randomSeed=1 1>/ddn/work/cjh/test/braker-2.1.6/tests/test1/filterGenemark.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/filterGenemark.stderr
# Fri Jul 29 12:11:47 2022: Ensuring at least 4000 genes in training file
/app/redhat6/anaconda3/bin/python3 /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/ensure_n_training_genes.py --goodGenes /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.f.good.gtf --badGenes /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.f.bad.gtf --N 4000 1>/ddn/work/cjh/test/braker-2.1.6/tests/test1/ensure_min_n_training_genes.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/ensure_min_n_training_genes.stderr
#Fri Jul 29 12:11:47 2022: downsampling good genemark genes according to poisson distribution with Lambda 2:
perl /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/downsample_traingenes.pl --in_gtf=/ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.f.good.gtf --out_gtf=/ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.d.gtf --lambda=2 1> /ddn/work/cjh/test/braker-2.1.6/tests/test1/downsample_traingenes.log 2> /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/downsample_traingenes.err
#**********************************************************************************
# TRAIN AUGUSTUS
#**********************************************************************************
# Fri Jul 29 12:11:47 2022: training AUGUSTUS
# Fri Jul 29 12:11:47 2022: creating softlink from /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf to /ddn/work/cjh/test/braker-2.1.6/tests/test1/traingenes.gtf.
ln -s /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf /ddn/work/cjh/test/braker-2.1.6/tests/test1/traingenes.gtf
# Fri Jul 29 12:11:47 2022: Converting gtf file /ddn/work/cjh/test/braker-2.1.6/tests/test1/traingenes.gtf to genbank file
# Fri Jul 29 12:11:47 2022: Computing flanking region size for AUGUSTUS training genes
# Fri Jul 29 12:11:47 2022: create genbank file /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.gb
perl /app/redhat6/augustus/augustus-3.4.0/scripts/gff2gbSmallDNA.pl /ddn/work/cjh/test/braker-2.1.6/tests/test1/traingenes.gtf /ddn/work/cjh/test/braker-2.1.6/tests/test1/genome.fa 1939 /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.gb 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/traingenes.gtf_gff2gbSmallDNA.stderr
#*********
# INFORMATION: the size of flanking region used in this BRAKER run is 1939. You might need this value if you later add a UTR training on top of an already existing BRAKER run.
#*********
# Fri Jul 29 12:11:51 2022: Genbank format file /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.gb contains 1028 genes.
# Fri Jul 29 12:11:51 2022: concatenating good and downsampled GeneMark training genes to /ddn/work/cjh/test/braker-2.1.6/tests/test1/good_genes.lst.
cat /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.d.gtf > /ddn/work/cjh/test/braker-2.1.6/tests/test1/good_genes.lst
# Fri Jul 29 12:11:51 2022: Filtering train.gb for "good" mRNAs:
perl /app/redhat6/augustus/augustus-3.4.0/scripts/filterGenesIn_mRNAname.pl /ddn/work/cjh/test/braker-2.1.6/tests/test1/good_genes.lst /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.gb > /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.f.gb 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/filterGenesIn_mRNAname.stderr
# Fri Jul 29 12:11:52 2022: Genbank format file /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.f.gb contains 702 genes.
# Fri Jul 29 12:11:52 2022: Running etraining to catch gene structure inconsistencies:
/app/redhat6/augustus/augustus-3.4.0/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-3.4.0/config /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.f.gb 1> /ddn/work/cjh/test/braker-2.1.6/tests/test1/gbFilterEtraining.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/gbFilterEtraining.stderr
Could you let me know what the problem is? Thanks in advance.
Are you running the latest code from Github for both Braker and Augustus? If not, please git clone, compile Augustus and try again.
Justin Choi @.***> schrieb am Fr. 29. Juli 2022 um 08:02:
I ran test1.sh in the example and got core dumped.
cat test1.log
Fri Jul 29 10:58:50 2022: Log information is stored in file /ddn/work/cjh/test/braker-2.1.6/tests/test1/braker.log
sh: line 1: 126276 Segmentation fault (core dumped) /app/redhat6/augustus/augustus-3.4.0/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-3.4.0/config /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.f.gb > /ddn/work/cjh/test/braker-2.1.6/tests/test1/gbFilterEtraining.stdout 2> /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/gbFilterEtraining.stderr ERROR in file /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/braker.pl at line 7468 Failed to execute: /app/redhat6/augustus/augustus-3.4.0/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-3.4.0/config /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.f.gb 1> /ddn/work/cjh/test/braker-2.1.6/tests/test1/gbFilterEtraining.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/gbFilterEtraining.stderr
real 73m2.617s user 20m38.514s sys 295m9.583s
cat test1/braker.log
#**********************************************************************************
BRAKER CONFIGURATION
#********************************************************************************** BRAKER CALL: /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/braker.pl --genome=../genome.fa --bam=../RNAseq.bam --softmasking --workingdir=test1 --cores 8 --gm_max_intergenic 10000 Fri Jul 29 10:58:49 2022: braker.pl version 2.1.6 Fri Jul 29 10:58:49 2022: Creating directory /ddn/work/cjh/test/braker-2.1.6/tests/test1. Fri Jul 29 10:58:49 2022: Configuring of BRAKER for using external tools... Fri Jul 29 10:58:49 2022: Found environment variable $AUGUSTUS_CONFIG_PATH. Setting $AUGUSTUS_CONFIG_PATH to /app/redhat6/augustus/augustus-3.4.0/config Fri Jul 29 10:58:49 2022: Found environment variable $AUGUSTUS_BIN_PATH. Setting $AUGUSTUS_BIN_PATH to /app/redhat6/augustus/augustus-3.4.0/bin Fri Jul 29 10:58:49 2022: Found environment variable $AUGUSTUS_SCRIPTS_PATH. Setting $AUGUSTUS_SCRIPTS_PATH to /app/redhat6/augustus/augustus-3.4.0/scripts Fri Jul 29 10:58:49 2022: Found environment variable $PYTHON3_PATH. Setting $PYTHON3_PATH to /app/redhat6/anaconda3/bin Fri Jul 29 10:58:49 2022: Found environment variable $GENEMARK_PATH. Setting $GENEMARK_PATH to /app/redhat6/gmes/GeneMark-4.64_lic Fri Jul 29 10:58:49 2022: Found environment variable $BAMTOOLS_PATH. Setting $BAMTOOLS_PATH to /app/redhat6/bamtools/bamtools-2.5.1/bin Fri Jul 29 10:58:49 2022: Found environment variable $SAMTOOLS_PATH. Setting $SAMTOOLS_PATH to /app/redhat6/samtools/samtools-1.14/bin Fri Jul 29 10:58:49 2022: Found environment variable $DIAMOND_PATH. Setting $DIAMOND_PATH to /app/redhat6/diamond/diamond-0.9.24 Fri Jul 29 10:58:49 2022: Found environment variable $CDBTOOLS_PATH. Setting $CDBTOOLS_PATH to /app/redhat6/cdbfasta/cdbfasta-1.00
#********* 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 Jul 29 10:58:50 2022: creating file that contains citations for this BRAKER run at /ddn/work/cjh/test/braker-2.1.6/tests/test1/what-to-cite.txt... Fri Jul 29 10:58:50 2022: create working directory /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET.
mkdir /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET Fri Jul 29 10:58:50 2022: create working directory /ddn/work/cjh/test/braker-2.1.6/tests/test1/species
mkdir /ddn/work/cjh/test/braker-2.1.6/tests/test1/species Fri Jul 29 10:58:50 2022: create working directory /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors
mkdir /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors Fri Jul 29 10:58:50 2022: changing into working directory /ddn/work/cjh/test/braker-2.1.6/tests/test1
cd /ddn/work/cjh/test/braker-2.1.6/tests/test1 Fri Jul 29 10:58:50 2022: Creating parameter template files for AUGUSTUS with new_species.pl Fri Jul 29 10:58:50 2022: new_species.pl will create parameter files for species Sp_1 in /app/redhat6/augustus/augustus-3.4.0/config/species/Sp_1
perl /app/redhat6/augustus/augustus-3.4.0/scripts/new_species.pl --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-3.4.0/config 1> /dev/null 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/new_species.stderr Fri Jul 29 10:58:50 2022: check_fasta_headers(): Checking fasta headers of file /ddn/work/cjh/test/braker-2.1.6/tests/../genome.fa
#********************************************************************************** PROCESSING HINTS
#********************************************************************************** Fri Jul 29 10:58:50 2022: Converting bam files to hints Fri Jul 29 10:58:50 2022: Checking bam headers Fri Jul 29 10:58:50 2022: create header file /ddn/work/cjh/test/braker-2.1.6/tests/test1/RNAseq_header.sam
/app/redhat6/bamtools/bamtools-2.5.1/bin/bamtools header -in /ddn/work/cjh/test/braker-2.1.6/tests/../RNAseq.bam > /ddn/work/cjh/test/braker-2.1.6/tests/test1/RNAseq_header.sam Fri Jul 29 10:58:50 2022: Deleting SAM header file /ddn/work/cjh/test/braker-2.1.6/tests/test1/RNAseq_header.sam (will not be needed from here on) Fri Jul 29 10:58:50 2022: Deleting /ddn/work/cjh/test/braker-2.1.6/tests/test1/RNAseq_new_header.sam Fri Jul 29 10:58:50 2022: make hints from BAM file /ddn/work/cjh/test/braker-2.1.6/tests/../RNAseq.bam
/app/redhat6/augustus/augustus-3.4.0/bin/bam2hints --intronsonly --in=/ddn/work/cjh/test/braker-2.1.6/tests/../RNAseq.bam --out=/ddn/work/cjh/test/braker-2.1.6/tests/test1/bam2hints.temp.0.gff 1> /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/bam2hints.0.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/bam2hints.0.stderr Fri Jul 29 10:59:05 2022: add hints from BAM file /ddn/work/cjh/test/braker-2.1.6/tests/../RNAseq.bam to hints file
cat /ddn/work/cjh/test/braker-2.1.6/tests/test1/bam2hints.temp.0.gff
/ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.temp.gff Fri Jul 29 10:59:05 2022: Checking for hints of src=C and with grp tags that should not be joined according to multiplicity Fri Jul 29 10:59:05 2022: Joining hints that are identical (& from the same source) into multiplicity hints (input file /ddn/work/cjh/test/braker-2.1.6/tests/test1/tmp_merge_hints.gff) Fri Jul 29 10:59:05 2022: sort hints of type rnaseq
cat /ddn/work/cjh/test/braker-2.1.6/tests/test1/tmp_merge_hints.gff | sort -n -k 4,4 | sort -s -n -k 5,5 | sort -s -n -k 3,3 | sort -s -k 1,1
/ddn/work/cjh/test/braker-2.1.6/tests/test1/hints.rnaseq.temp.sort.gff Fri Jul 29 10:59:05 2022: join multiple hints
perl /app/redhat6/augustus/augustus-3.4.0/scripts/join_mult_hints.pl </ddn/work/cjh/test/braker-2.1.6/tests/test1/hints.rnaseq.temp.sort.gff
/ddn/work/cjh/test/braker-2.1.6/tests/test1/tmp_merge_hints.gff 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/join_mult_hints.rnaseq.stderr mv /ddn/work/cjh/test/braker-2.1.6/tests/test1/tmp_merge_hints.gff /ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.temp.gff Fri Jul 29 10:59:06 2022: filter introns, find strand and change score to 'mult' entry
perl /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/filterIntronsFindStrand.pl /ddn/work/cjh/test/braker-2.1.6/tests/test1/genome.fa /ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.temp.gff --score 1>>/ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.gff 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/filterIntronsFindStrand.stderr Fri Jul 29 10:59:06 2022: rm /ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.temp.gff Fri Jul 29 10:59:06 2022: Preparing hints for running GeneMark Fri Jul 29 10:59:06 2022: Filtering intron hints for GeneMark from /ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.gff...
cat /ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff.rnaseq | sort -n -k 4,4 | sort -s -n -k 5,5 | sort -s -k 3,3 | sort -s -k 1,1 | /app/redhat6/augustus/augustus-3.4.0/scripts/join_mult_hints.pl > /ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff.rnaseq.tmp mv /ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff.rnaseq.tmp /ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff
#********************************************************************************** RUNNING GENEMARK-EX
#********************************************************************************** Fri Jul 29 11:02:27 2022: Checking whether file /ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff contains enough hints and sufficient multiplicity information... Fri Jul 29 11:02:27 2022: Executing GeneMark-ET Fri Jul 29 11:02:27 2022: changing into GeneMark-ET directory /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET
cd /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET Fri Jul 29 11:02:27 2022: Executing gmes_petap.pl
perl /app/redhat6/gmes/GeneMark-4.64_lic/gmes_petap.pl --verbose --sequence=/ddn/work/cjh/test/braker-2.1.6/tests/test1/genome.fa --ET=/ddn/work/cjh/test/braker-2.1.6/tests/test1/genemark_hintsfile.gff --cores=8 --gc_donor 0.001 --soft_mask auto --max_intergenic=10000 1>/ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/GeneMark-ET.stderr Fri Jul 29 12:11:46 2022: change to working directory /ddn/work/cjh/test/braker-2.1.6/tests/test1
cd /ddn/work/cjh/test/braker-2.1.6/tests/test1 Fri Jul 29 12:11:46 2022: Filtering output of GeneMark for generating training genes for AUGUSTUS Fri Jul 29 12:11:46 2022: Checking whether hintsfile contains single exon CDSpart hints or start/stop hints Fri Jul 29 12:11:46 2022: sorting GeneMark predictions in /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf
/app/redhat6/anaconda3/bin/python3 /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/sortGeneMark.py /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf > /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf.sorted 2> /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/sortGeneMark.err mv /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf.sorted /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf Fri Jul 29 12:11:47 2022: filtering GeneMark genes by intron hints
perl /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/filterGenemark.pl --genemark=/ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf --hints=/ddn/work/cjh/test/braker-2.1.6/tests/test1/hintsfile.gff --randomSeed=1 1>/ddn/work/cjh/test/braker-2.1.6/tests/test1/filterGenemark.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/filterGenemark.stderr Fri Jul 29 12:11:47 2022: Ensuring at least 4000 genes in training file
/app/redhat6/anaconda3/bin/python3 /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/ensure_n_training_genes.py --goodGenes /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.f.good.gtf --badGenes /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.f.bad.gtf --N 4000 1>/ddn/work/cjh/test/braker-2.1.6/tests/test1/ensure_min_n_training_genes.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/ensure_min_n_training_genes.stderr #Fri Jul 29 12:11:47 2022: downsampling good genemark genes according to poisson distribution with Lambda 2: perl /app/redhat6/BRAKER/BRAKER-2.1.6/scripts/downsample_traingenes.pl --in_gtf=/ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.f.good.gtf --out_gtf=/ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.d.gtf --lambda=2 1> /ddn/work/cjh/test/braker-2.1.6/tests/test1/downsample_traingenes.log 2> /ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/downsample_traingenes.err
#********************************************************************************** TRAIN AUGUSTUS
#********************************************************************************** Fri Jul 29 12:11:47 2022: training AUGUSTUS Fri Jul 29 12:11:47 2022: creating softlink from /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf to /ddn/work/cjh/test/braker-2.1.6/tests/test1/traingenes.gtf.
ln -s /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.gtf /ddn/work/cjh/test/braker-2.1.6/tests/test1/traingenes.gtf Fri Jul 29 12:11:47 2022: Converting gtf file /ddn/work/cjh/test/braker-2.1.6/tests/test1/traingenes.gtf to genbank file Fri Jul 29 12:11:47 2022: Computing flanking region size for AUGUSTUS training genes Fri Jul 29 12:11:47 2022: create genbank file /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.gb
perl /app/redhat6/augustus/augustus-3.4.0/scripts/gff2gbSmallDNA.pl /ddn/work/cjh/test/braker-2.1.6/tests/test1/traingenes.gtf /ddn/work/cjh/test/braker-2.1.6/tests/test1/genome.fa 1939 /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.gb 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/traingenes.gtf_gff2gbSmallDNA.stderr #********* INFORMATION: the size of flanking region used in this BRAKER run is 1939. You might need this value if you later add a UTR training on top of an already existing BRAKER run.
#********* Fri Jul 29 12:11:51 2022: Genbank format file /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.gb contains 1028 genes. Fri Jul 29 12:11:51 2022: concatenating good and downsampled GeneMark training genes to /ddn/work/cjh/test/braker-2.1.6/tests/test1/good_genes.lst.
cat /ddn/work/cjh/test/braker-2.1.6/tests/test1/GeneMark-ET/genemark.d.gtf
/ddn/work/cjh/test/braker-2.1.6/tests/test1/good_genes.lst Fri Jul 29 12:11:51 2022: Filtering train.gb for "good" mRNAs:
perl /app/redhat6/augustus/augustus-3.4.0/scripts/filterGenesIn_mRNAname.pl /ddn/work/cjh/test/braker-2.1.6/tests/test1/good_genes.lst /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.gb > /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.f.gb 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/filterGenesIn_mRNAname.stderr Fri Jul 29 12:11:52 2022: Genbank format file /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.f.gb contains 702 genes. Fri Jul 29 12:11:52 2022: Running etraining to catch gene structure inconsistencies:
/app/redhat6/augustus/augustus-3.4.0/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-3.4.0/config /ddn/work/cjh/test/braker-2.1.6/tests/test1/train.f.gb 1> /ddn/work/cjh/test/braker-2.1.6/tests/test1/gbFilterEtraining.stdout 2>/ddn/work/cjh/test/braker-2.1.6/tests/test1/errors/gbFilterEtraining.stderr
Could you let me know what the problem is? Thanks in advance.
— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/508, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JD6HN5DM56POYMMNPTVWNXXTANCNFSM547SZOTQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
I am encountering the same error.
braker.pl --genome=mygenome.fasta --species=My_species --bam=my.sorted.bam --workingdir=braker --softmasking --UTR=on --cores=40
This command creates a "My_species" directory in ${AUGUSTUS_CONFIG_PATH}/species. But the directory is gone when the program stops.
cat gbFilterEtraining.stderr
Could not find the config file /home/XXX/augustus_config/species/My_species/My_species_parameters.cfg.
Looking for My_species_parameters.cfg in the configuration directory instead ... not found.
cat gbFilterEtraining.stdout
Species-specific configuration files not found in /home/XXX/augustus_config/species/. Type "augustus --species=help" to see available species.
I am using Augustus and braker downloaded from Github on 14th Jul. Thank you in advance.
Yes, please use git clone for both Augustus and Braker to confirm.
Justin Choi @.***> schrieb am Di. 2. Aug. 2022 um 02:41:
@KatharinaHoff https://github.com/KatharinaHoff I used release 2.1.6. Should I use git clone?
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I used git clone for braker and augustus, but still got the error.
> cat test1.log
Wed Aug 10 14:50:38 2022: Log information is stored in file /ddn/work/cjh/test/braker-20220128/tests/test1/braker.log
sh: line 1: 146169 Segmentation fault (core dumped) /app/redhat6/augustus/augustus-20220316/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-20220316/config /ddn/work/cjh/test/braker-20220128/tests/test1/train.f.gb > /ddn/work/cjh/test/braker-20220128/tests/test1/gbFilterEtraining.stdout 2> /ddn/work/cjh/test/braker-20220128/tests/test1/errors/gbFilterEtraining.stderr
ERROR in file /app/redhat6/BRAKER/BRAKER-20220128/scripts/braker.pl at line 7493
Failed to execute: /app/redhat6/augustus/augustus-20220316/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-20220316/config /ddn/work/cjh/test/braker-20220128/tests/test1/train.f.gb 1> /ddn/work/cjh/test/braker-20220128/tests/test1/gbFilterEtraining.stdout 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/gbFilterEtraining.stderr
real 5m44.471s
user 19m30.830s
sys 0m23.691s
> cat test1/braker.log
#**********************************************************************************
# BRAKER CONFIGURATION
#**********************************************************************************
# BRAKER CALL: /app/redhat6/BRAKER/BRAKER-20220128/scripts/braker.pl --genome=../genome.fa --bam=../RNAseq.bam --softmasking --workingdir=test1 --cores 8 --gm_max_intergenic 10000
# Wed Aug 10 15:06:13 2022: braker.pl version 2.1.6
# Wed Aug 10 15:06:13 2022: Creating directory /ddn/work/cjh/test/braker-20220128/tests/test1.
# Wed Aug 10 15:06:13 2022: Configuring of BRAKER for using external tools...
# Wed Aug 10 15:06:13 2022: Found environment variable $AUGUSTUS_CONFIG_PATH. Setting $AUGUSTUS_CONFIG_PATH to /app/redhat6/augustus/augustus-20220316/config
# Wed Aug 10 15:06:13 2022: Found environment variable $AUGUSTUS_BIN_PATH. Setting $AUGUSTUS_BIN_PATH to /app/redhat6/augustus/augustus-20220316/bin
# Wed Aug 10 15:06:13 2022: Found environment variable $AUGUSTUS_SCRIPTS_PATH. Setting $AUGUSTUS_SCRIPTS_PATH to /app/redhat6/augustus/augustus-20220316/scripts
# Wed Aug 10 15:06:13 2022: Found environment variable $PYTHON3_PATH. Setting $PYTHON3_PATH to /app/redhat6/anaconda3/bin
# Wed Aug 10 15:06:13 2022: Found environment variable $GENEMARK_PATH. Setting $GENEMARK_PATH to /app/redhat6/gmes/GeneMark-4.64_lic
# Wed Aug 10 15:06:13 2022: Found environment variable $BAMTOOLS_PATH. Setting $BAMTOOLS_PATH to /app/redhat6/bamtools/bamtools-2.5.1/bin
# Wed Aug 10 15:06:13 2022: Found environment variable $SAMTOOLS_PATH. Setting $SAMTOOLS_PATH to /app/redhat6/samtools/samtools-1.14/bin
# Wed Aug 10 15:06:13 2022: Found environment variable $DIAMOND_PATH. Setting $DIAMOND_PATH to /app/redhat6/diamond/diamond-0.9.24
# Wed Aug 10 15:06:13 2022: Found environment variable $CDBTOOLS_PATH. Setting $CDBTOOLS_PATH to /app/redhat6/cdbfasta/cdbfasta-1.00
#*********
# 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
#**********************************************************************************
# Wed Aug 10 15:06:13 2022: creating file that contains citations for this BRAKER run at /ddn/work/cjh/test/braker-20220128/tests/test1/what-to-cite.txt...
# Wed Aug 10 15:06:13 2022: create working directory /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET.
mkdir /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET
# Wed Aug 10 15:06:13 2022: create working directory /ddn/work/cjh/test/braker-20220128/tests/test1/species
mkdir /ddn/work/cjh/test/braker-20220128/tests/test1/species
# Wed Aug 10 15:06:13 2022: create working directory /ddn/work/cjh/test/braker-20220128/tests/test1/errors
mkdir /ddn/work/cjh/test/braker-20220128/tests/test1/errors
# Wed Aug 10 15:06:14 2022: changing into working directory /ddn/work/cjh/test/braker-20220128/tests/test1
cd /ddn/work/cjh/test/braker-20220128/tests/test1
# Wed Aug 10 15:06:14 2022: Creating parameter template files for AUGUSTUS with new_species.pl
# Wed Aug 10 15:06:14 2022: new_species.pl will create parameter files for species Sp_1 in /app/redhat6/augustus/augustus-20220316/config/species/Sp_1
perl /app/redhat6/augustus/augustus-20220316/scripts/new_species.pl --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-20220316/config 1> /dev/null 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/new_species.stderr
# Wed Aug 10 15:06:14 2022: check_fasta_headers(): Checking fasta headers of file /ddn/work/cjh/test/braker-20220128/tests/../genome.fa
#**********************************************************************************
# PROCESSING HINTS
#**********************************************************************************
# Wed Aug 10 15:06:14 2022: Converting bam files to hints
# Wed Aug 10 15:06:14 2022: Checking bam headers
# Wed Aug 10 15:06:14 2022: create header file /ddn/work/cjh/test/braker-20220128/tests/test1/RNAseq_header.sam
/app/redhat6/bamtools/bamtools-2.5.1/bin/bamtools header -in /ddn/work/cjh/test/braker-20220128/tests/../RNAseq.bam > /ddn/work/cjh/test/braker-20220128/tests/test1/RNAseq_header.sam
# Wed Aug 10 15:06:14 2022: Deleting SAM header file /ddn/work/cjh/test/braker-20220128/tests/test1/RNAseq_header.sam (will not be needed from here on)
# Wed Aug 10 15:06:14 2022: Deleting /ddn/work/cjh/test/braker-20220128/tests/test1/RNAseq_new_header.sam
# Wed Aug 10 15:06:14 2022: make hints from BAM file /ddn/work/cjh/test/braker-20220128/tests/../RNAseq.bam
/app/redhat6/augustus/augustus-20220316/bin/bam2hints --intronsonly --in=/ddn/work/cjh/test/braker-20220128/tests/../RNAseq.bam --out=/ddn/work/cjh/test/braker-20220128/tests/test1/bam2hints.temp.0.gff 1> /ddn/work/cjh/test/braker-20220128/tests/test1/errors/bam2hints.0.stdout 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/bam2hints.0.stderr
# Wed Aug 10 15:06:21 2022: add hints from BAM file /ddn/work/cjh/test/braker-20220128/tests/../RNAseq.bam to hints file
cat /ddn/work/cjh/test/braker-20220128/tests/test1/bam2hints.temp.0.gff >>/ddn/work/cjh/test/braker-20220128/tests/test1/hintsfile.temp.gff
# Wed Aug 10 15:06:21 2022: Checking for hints of src=C and with grp tags that should not be joined according to multiplicity
# Wed Aug 10 15:06:21 2022: Joining hints that are identical (& from the same source) into multiplicity hints (input file /ddn/work/cjh/test/braker-20220128/tests/test1/tmp_merge_hints.gff)
# Wed Aug 10 15:06:21 2022: sort hints of type rnaseq
cat /ddn/work/cjh/test/braker-20220128/tests/test1/tmp_merge_hints.gff | sort -n -k 4,4 | sort -s -n -k 5,5 | sort -s -n -k 3,3 | sort -s -k 1,1 >/ddn/work/cjh/test/braker-20220128/tests/test1/hints.rnaseq.temp.sort.gff
# Wed Aug 10 15:06:22 2022: join multiple hints
perl /app/redhat6/augustus/augustus-20220316/scripts/join_mult_hints.pl </ddn/work/cjh/test/braker-20220128/tests/test1/hints.rnaseq.temp.sort.gff >/ddn/work/cjh/test/braker-20220128/tests/test1/tmp_merge_hints.gff 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/join_mult_hints.rnaseq.stderr
mv /ddn/work/cjh/test/braker-20220128/tests/test1/tmp_merge_hints.gff /ddn/work/cjh/test/braker-20220128/tests/test1/hintsfile.temp.gff
# Wed Aug 10 15:06:22 2022: filter introns, find strand and change score to 'mult' entry
perl /app/redhat6/BRAKER/BRAKER-20220128/scripts/filterIntronsFindStrand.pl /ddn/work/cjh/test/braker-20220128/tests/test1/genome.fa /ddn/work/cjh/test/braker-20220128/tests/test1/hintsfile.temp.gff --score 1>>/ddn/work/cjh/test/braker-20220128/tests/test1/hintsfile.gff 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/filterIntronsFindStrand.stderr
# Wed Aug 10 15:06:22 2022: rm /ddn/work/cjh/test/braker-20220128/tests/test1/hintsfile.temp.gff
# Wed Aug 10 15:06:22 2022: Preparing hints for running GeneMark
# Wed Aug 10 15:06:22 2022: Filtering intron hints for GeneMark from /ddn/work/cjh/test/braker-20220128/tests/test1/hintsfile.gff...
cat /ddn/work/cjh/test/braker-20220128/tests/test1/genemark_hintsfile.gff.rnaseq | sort -n -k 4,4 | sort -s -n -k 5,5 | sort -s -k 3,3 | sort -s -k 1,1 | /app/redhat6/augustus/augustus-20220316/scripts/join_mult_hints.pl > /ddn/work/cjh/test/braker-20220128/tests/test1/genemark_hintsfile.gff.rnaseq.tmp
mv /ddn/work/cjh/test/braker-20220128/tests/test1/genemark_hintsfile.gff.rnaseq.tmp /ddn/work/cjh/test/braker-20220128/tests/test1/genemark_hintsfile.gff
#**********************************************************************************
# RUNNING GENEMARK-EX
#**********************************************************************************
# Wed Aug 10 15:06:22 2022: Checking whether file /ddn/work/cjh/test/braker-20220128/tests/test1/genemark_hintsfile.gff contains enough hints and sufficient multiplicity information...
# Wed Aug 10 15:06:22 2022: Executing GeneMark-ET
# Wed Aug 10 15:06:22 2022: changing into GeneMark-ET directory /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET
cd /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET
# Wed Aug 10 15:06:22 2022: Executing gmes_petap.pl
perl /app/redhat6/gmes/GeneMark-4.64_lic/gmes_petap.pl --verbose --sequence=/ddn/work/cjh/test/braker-20220128/tests/test1/genome.fa --ET=/ddn/work/cjh/test/braker-20220128/tests/test1/genemark_hintsfile.gff --cores=8 --gc_donor 0.001 --soft_mask auto --max_intergenic=10000 1>/ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET.stdout 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/GeneMark-ET.stderr
# Wed Aug 10 15:11:43 2022: change to working directory /ddn/work/cjh/test/braker-20220128/tests/test1
cd /ddn/work/cjh/test/braker-20220128/tests/test1
# Wed Aug 10 15:11:43 2022: Filtering output of GeneMark for generating training genes for AUGUSTUS
# Wed Aug 10 15:11:43 2022: Checking whether hintsfile contains single exon CDSpart hints or start/stop hints
# Wed Aug 10 15:11:43 2022: sorting GeneMark predictions in /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.gtf
/app/redhat6/anaconda3/bin/python3 /app/redhat6/BRAKER/BRAKER-20220128/scripts/sortGeneMark.py /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.gtf > /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.gtf.sorted 2> /ddn/work/cjh/test/braker-20220128/tests/test1/errors/sortGeneMark.err
mv /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.gtf.sorted /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.gtf
# Wed Aug 10 15:11:44 2022: filtering GeneMark genes by intron hints
perl /app/redhat6/BRAKER/BRAKER-20220128/scripts/filterGenemark.pl --genemark=/ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.gtf --hints=/ddn/work/cjh/test/braker-20220128/tests/test1/hintsfile.gff --randomSeed=1 1>/ddn/work/cjh/test/braker-20220128/tests/test1/filterGenemark.stdout 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/filterGenemark.stderr
# Wed Aug 10 15:11:44 2022: Ensuring at least 4000 genes in training file
/app/redhat6/anaconda3/bin/python3 /app/redhat6/BRAKER/BRAKER-20220128/scripts/ensure_n_training_genes.py --goodGenes /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.f.good.gtf --badGenes /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.f.bad.gtf --N 4000 1>/ddn/work/cjh/test/braker-20220128/tests/test1/ensure_min_n_training_genes.stdout 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/ensure_min_n_training_genes.stderr
#Wed Aug 10 15:11:44 2022: downsampling good genemark genes according to poisson distribution with Lambda 2:
perl /app/redhat6/BRAKER/BRAKER-20220128/scripts/downsample_traingenes.pl --in_gtf=/ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.f.good.gtf --out_gtf=/ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.d.gtf --lambda=2 1> /ddn/work/cjh/test/braker-20220128/tests/test1/downsample_traingenes.log 2> /ddn/work/cjh/test/braker-20220128/tests/test1/errors/downsample_traingenes.err
#**********************************************************************************
# TRAIN AUGUSTUS
#**********************************************************************************
# Wed Aug 10 15:11:44 2022: training AUGUSTUS
# Wed Aug 10 15:11:44 2022: creating softlink from /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.gtf to /ddn/work/cjh/test/braker-20220128/tests/test1/traingenes.gtf.
ln -s /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.gtf /ddn/work/cjh/test/braker-20220128/tests/test1/traingenes.gtf
# Wed Aug 10 15:11:44 2022: Converting gtf file /ddn/work/cjh/test/braker-20220128/tests/test1/traingenes.gtf to genbank file
# Wed Aug 10 15:11:44 2022: Computing flanking region size for AUGUSTUS training genes
# Wed Aug 10 15:11:44 2022: create genbank file /ddn/work/cjh/test/braker-20220128/tests/test1/train.gb
perl /app/redhat6/augustus/augustus-20220316/scripts/gff2gbSmallDNA.pl /ddn/work/cjh/test/braker-20220128/tests/test1/traingenes.gtf /ddn/work/cjh/test/braker-20220128/tests/test1/genome.fa 1939 /ddn/work/cjh/test/braker-20220128/tests/test1/train.gb 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/traingenes.gtf_gff2gbSmallDNA.stderr
#*********
# INFORMATION: the size of flanking region used in this BRAKER run is 1939. You might need this value if you later add a UTR training on top of an already existing BRAKER run.
#*********
# Wed Aug 10 15:11:48 2022: Genbank format file /ddn/work/cjh/test/braker-20220128/tests/test1/train.gb contains 1028 genes.
# Wed Aug 10 15:11:48 2022: concatenating good and downsampled GeneMark training genes to /ddn/work/cjh/test/braker-20220128/tests/test1/good_genes.lst.
cat /ddn/work/cjh/test/braker-20220128/tests/test1/GeneMark-ET/genemark.d.gtf > /ddn/work/cjh/test/braker-20220128/tests/test1/good_genes.lst
# Wed Aug 10 15:11:48 2022: Filtering train.gb for "good" mRNAs:
perl /app/redhat6/augustus/augustus-20220316/scripts/filterGenesIn_mRNAname.pl /ddn/work/cjh/test/braker-20220128/tests/test1/good_genes.lst /ddn/work/cjh/test/braker-20220128/tests/test1/train.gb > /ddn/work/cjh/test/braker-20220128/tests/test1/train.f.gb 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/filterGenesIn_mRNAname.stderr
# Wed Aug 10 15:11:48 2022: Genbank format file /ddn/work/cjh/test/braker-20220128/tests/test1/train.f.gb contains 702 genes.
# Wed Aug 10 15:11:48 2022: Running etraining to catch gene structure inconsistencies:
/app/redhat6/augustus/augustus-20220316/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-20220316/config /ddn/work/cjh/test/braker-20220128/tests/test1/train.f.gb 1> /ddn/work/cjh/test/braker-20220128/tests/test1/gbFilterEtraining.stdout 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/gbFilterEtraining.stderr
@KatharinaHoff Could you have time to guide me how to resolve this issue?
This appears to be an error in AUGUSTUS. If you could upload the input files to the command that crashes: /app/redhat6/augustus/augustus-20220316/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-20220316/config /ddn/work/cjh/test/braker-20220128/tests/test1/train.f.gb and I can reproduce the segmentation fault, then I should be able to diagnose it and fix it. Please make sure to include the (gzipped) folder /app/redhat6/augustus/augustus-20220316/config/species/Sp_1
Am Mi., 10. Aug. 2022 um 08:07 Uhr schrieb Justin Choi < @.***>:
I used git clone for braker and augustus, but still got the error.
cat test1.log
Wed Aug 10 14:50:38 2022: Log information is stored in file /ddn/work/cjh/test/braker-20220128/tests/test1/braker.log
sh: line 1: 146169 Segmentation fault (core dumped) /app/redhat6/augustus/augustus-20220316/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-20220316/config /ddn/work/cjh/test/braker-20220128/tests/test1/train.f.gb > /ddn/work/cjh/test/braker-20220128/tests/test1/gbFilterEtraining.stdout 2> /ddn/work/cjh/test/braker-20220128/tests/test1/errors/gbFilterEtraining.stderr ERROR in file /app/redhat6/BRAKER/BRAKER-20220128/scripts/braker.pl at line 7493 Failed to execute: /app/redhat6/augustus/augustus-20220316/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-20220316/config /ddn/work/cjh/test/braker-20220128/tests/test1/train.f.gb 1> /ddn/work/cjh/test/braker-20220128/tests/test1/gbFilterEtraining.stdout 2>/ddn/work/cjh/test/braker-20220128/tests/test1/errors/gbFilterEtraining.stderr
real 5m44.471s user 19m30.830s sys 0m23.691s
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train.f.gb.gz @MarioStanke Thanks a lot for your reply. While preparing a file, there is no Sp_1 in /app/redhat6/augustus/augustus-20220316/config/species/. Is that the problem?
As shown in braker.log, Sp_1 was created using new_species.pl, but removed somehow before running etraining. So I ran etraining after running new_species.pl, but etraing was failed again.
Please check whether
perl /app/redhat6/augustus/augustus-3.4.0/scripts/new_species.pl --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-3.4.0/config
throws an error on your system. Possibly, you don't have writing permissions in your /app/redhat6/augustus/augustus-3.4.0/config directory?