Entering edit mode
2.8 years ago
vizzerraa
•
0
Hi, BRAKER2 (v.2.1.6) is not producing the "genemark_hintsfile.gff.prot.tmp" file after ProtHint finishes, what could be causing this issue?
The full command was
/data/selaginella/anaconda3/envs/braker2_conda_env/BRAKER-2.1.6/scripts/braker.pl --genome=/data/selaginella/DATA/annotations/braker_wallacei_test/a.lines.fa --bam=/data/selaginella/DATA/annotations/braker_wallacei_test/wallacei.sorted.bam --species=wallacei --prot_seq=/data/selaginella/DATA/annotations/braker_wallacei_test/protein.fa --ALIGNMENT_TOOL_PATH=/data/selaginella/anaconda3/envs/braker2_conda_env/gth-1.7.3-Linux_x86_64-64bit/bin --GENEMARK_PATH=/data/selaginella/anaconda3/envs/braker2_conda_env/gmes_linux_64/ --AUGUSTUS_SCRIPTS_PATH=/data/selaginella/anaconda3/envs/braker2_conda_env/augustus-3.4.0/scripts --GUSHR_PATH=/data/selaginella/anaconda3/envs/braker2_conda_env/GUSHR --PROTHINT_PATH=/data/selaginella/anaconda3/envs/braker2_conda_env/ProtHint/bin --etpmode --UTR=on --softmasking --cores=8
Please find the braker.log attached below. There is no content in any of the error files either.
#**********************************************************************************
# BRAKER CONFIGURATION
#**********************************************************************************
# BRAKER CALL: /data/selaginella/anaconda3/envs/braker2_conda_env/BRAKER-2.1.6/scripts/braker.pl --genome=/data/selaginella/DATA/annotations/braker_wallacei_test/a.lines.fa --bam=/data/selaginella/DATA/annotations/braker_wallacei_test/wallacei.sorted.bam --species=wallacei --prot_seq=/data/selaginella/DATA/annotations/braker_wallacei_test/protein.fa --ALIGNMENT_TOOL_PATH=/data/selaginella/anaconda3/envs/braker2_conda_env/gth-1.7.3-Linux_x86_64-64bit/bin --GENEMARK_PATH=/data/selaginella/anaconda3/envs/braker2_conda_env/gmes_linux_64/ --AUGUSTUS_SCRIPTS_PATH=/data/selaginella/anaconda3/envs/braker2_conda_env/augustus-3.4.0/scripts --GUSHR_PATH=/data/selaginella/anaconda3/envs/braker2_conda_env/GUSHR --PROTHINT_PATH=/data/selaginella/anaconda3/envs/braker2_conda_env/ProtHint/bin --etpmode --UTR=on --softmasking --cores=8
# Wed Jun 16 21:54:15 2021: braker.pl version 2.1.6
# Wed Jun 16 21:54:15 2021: Configuring of BRAKER for using external tools...
# Wed Jun 16 21:54:15 2021: Trying to guess $AUGUSTUS_BIN_PATH from $AUGUSTUS_CONFIG_PATH.
# Wed Jun 16 21:54:15 2021: Setting $AUGUSTUS_BIN_PATH to /data/selaginella/anaconda3/envs/braker2_conda_env/bin/../config/../bin
# Wed Jun 16 21:54:15 2021: Setting $AUGUSTUS_SCRIPTS_PATH to command line argument --AUGUSTUS_SCRIPTS_PATH value /data/selaginella/anaconda3/envs/braker2_conda_env/augustus-3.4.0/scripts.
# Wed Jun 16 21:54:15 2021: Did not find environment variable $PYTHON3_PATH
# Wed Jun 16 21:54:15 2021: Trying to guess $PYTHON3_PATH from location of python3 executable that is available in your $PATH
# Wed Jun 16 21:54:15 2021: Setting $PYTHON3_PATH to /data/selaginella/anaconda3/envs/braker2_conda_env/bin
# Wed Jun 16 21:54:15 2021: Did not find environment variable $JAVA_PATH
# Wed Jun 16 21:54:15 2021: Trying to guess $JAVA_PATH from location of java executable that is available in your $PATH
# Wed Jun 16 21:54:15 2021: Setting $JAVA_PATH to /data/selaginella/miniconda3/bin
# Wed Jun 16 21:54:15 2021: Setting $GUSHR_PATH to command line argument --GUSHR_PATH value /data/selaginella/anaconda3/envs/braker2_conda_env/GUSHR.
# Wed Jun 16 21:54:15 2021: Setting $GENEMARK_PATH to command line argument --GENEMARK_PATH value /data/selaginella/anaconda3/envs/braker2_conda_env/gmes_linux_64.
# Wed Jun 16 21:54:15 2021: Did not find environment variable $BAMTOOLS_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.
# Wed Jun 16 21:54:15 2021: Trying to guess $BAMTOOLS_BIN_PATH from location of bamtools executable that is available in your $PATH
# Wed Jun 16 21:54:15 2021: Setting $BAMTOOLS_BIN_PATH to /data/selaginella/anaconda3/envs/braker2_conda_env/bin
# Wed Jun 16 21:54:15 2021: Did not find environment variable $SAMTOOLS_PATH (either variable does not exist, or the path given in variable doesnot exist). Will try to set this variable in a different way, later.
# Wed Jun 16 21:54:15 2021: Trying to guess $SAMTOOLS_PATH from location of samtools executable in your $PATH
# Wed Jun 16 21:54:15 2021: Setting $SAMTOOLS_PATH to /data/selaginella/miniconda3/bin
# Wed Jun 16 21:54:15 2021: Did not find environment variable $DIAMOND_PATH
# Wed Jun 16 21:54:15 2021: Trying to guess $DIAMOND_PATH from location of diamond executable that is available in your $PATH
# Wed Jun 16 21:54:15 2021: Setting $DIAMOND_PATH to /data/selaginella/anaconda3/envs/braker2_conda_env/bin
# Wed Jun 16 21:54:15 2021: Setting $PROTHINT_PATH to command line argument --PROTHINT_PATH value /data/selaginella/anaconda3/envs/braker2_conda_env/ProtHint/bin.
# Wed Jun 16 21:54:15 2021: Did not find environment variable $CDBTOOLS_PATH
# Wed Jun 16 21:54:15 2021: Trying to guess $CDBTOOLS_PATH from location of cdbfasta executable that is available in your $PATH
# Wed Jun 16 21:54:15 2021: Setting $CDBTOOLS_PATH to /data/selaginella/anaconda3/envs/braker2_conda_env/bin
#**********************************************************************************
# CREATING DIRECTORY STRUCTURE
#**********************************************************************************
# Wed Jun 16 21:54:15 2021: create working directory /data/selaginella/DATA/annotations/braker_wallacei_test/braker.
mkdir /data/selaginella/DATA/annotations/braker_wallacei_test/braker
# Wed Jun 16 21:54:15 2021: creating file that contains citations for this BRAKER run at /data/selaginella/DATA/annotations/braker_wallacei_test/braker/what-to-cite.txt...
# Wed Jun 16 21:54:15 2021: create working directory /data/selaginella/DATA/annotations/braker_wallacei_test/braker/GeneMark-ETP.
mkdir /data/selaginella/DATA/annotations/braker_wallacei_test/braker/GeneMark-ETP
# Wed Jun 16 21:54:15 2021: create working directory /data/selaginella/DATA/annotations/braker_wallacei_test/braker/GeneMark-ES.
mkdir /data/selaginella/DATA/annotations/braker_wallacei_test/braker/GeneMark-ES
# Wed Jun 16 21:54:15 2021: create working directory /data/selaginella/DATA/annotations/braker_wallacei_test/braker/species
mkdir /data/selaginella/DATA/annotations/braker_wallacei_test/braker/species
# Wed Jun 16 21:54:15 2021: create working directory /data/selaginella/DATA/annotations/braker_wallacei_test/braker/errors
mkdir /data/selaginella/DATA/annotations/braker_wallacei_test/braker/errors
# Wed Jun 16 21:54:15 2021: changing into working directory /data/selaginella/DATA/annotations/braker_wallacei_test/braker
cd /data/selaginella/DATA/annotations/braker_wallacei_test/braker
# Wed Jun 16 21:54:15 2021: Creating parameter template files for AUGUSTUS with new_species.pl
# Wed Jun 16 21:54:15 2021: new_species.pl will create parameter files for species wallacei in /data/selaginella/anaconda3/envs/braker2_conda_env/bin/../config/species/wallacei
perl /data/selaginella/anaconda3/envs/braker2_conda_env/augustus-3.4.0/scripts/new_species.pl --species=wallacei --AUGUSTUS_CONFIG_PATH=/data/selaginella/anaconda3/envs/braker2_conda_env/bin/../config 1> /dev/null 2>/data/selaginella/DATA/annotations/braker_wallacei_test/braker/errors/new_species.stderr
# Wed Jun 16 21:54:15 2021: check_fasta_headers(): Checking fasta headers of file /data/selaginella/DATA/annotations/braker_wallacei_test/a.lines.fa
#*********
# WARNING: Detected whitespace in fasta header of file /data/selaginella/DATA/annotations/braker_wallacei_test/a.lines.fa. This may later on cause problems! The pipeline will create a new file without spaces or "|" characters and a genome_header.map file to look up the old and new headers. This message will be suppressed from now on!
#*********
# Wed Jun 16 21:54:18 2021: check_fasta_headers(): Checking fasta headers of file /data/selaginella/DATA/annotations/braker_wallacei_test/protein.fa
#*********
# WARNING: Detected whitespace in fasta header of file /data/selaginella/DATA/annotations/braker_wallacei_test/protein.fa. This may later on cause problems! The pipeline will create a new file without spaces or "|" characters and a genome_header.map file to look up the old and new headers. This message will be suppressed from now on!
#*********
# Wed Jun 16 21:54:18 2021: Assuming that this is not a DNA fasta file because other characters than A, T, G, C, N, a, t, g, c, n were contained. If this is supposed to be a DNA fasta file, check the content of your file! If this is supposed to be a protein fasta file, please ignore this message!
#*********
# WARNING: in file /data/selaginella/anaconda3/envs/braker2_conda_env/BRAKER-2.1.6/scripts/braker.pl at line 1341
file /data/selaginella/DATA/annotations/braker_wallacei_test/braker/genome.fa contains a highly fragmented assembly (210069 scaffolds). This may lead to problems when running AUGUSTUS via braker in parallelized mode. You set --cores=8. You should run braker.pl in linear mode on such genomes, though (--cores=1).
#*********
#**********************************************************************************
# PROCESSING HINTS
#**********************************************************************************
# Wed Jun 16 21:54:19 2021: Running ProtHint to produce hints from protein sequence file (this may take a couple of hours)...
# Wed Jun 16 21:54:19 2021: Running Genemark-ES for ProtHint...
# Wed Jun 16 21:54:19 2021: Executing GeneMark-ES
# Wed Jun 16 21:54:19 2021: changing into GeneMark-ES directory /data/selaginella/DATA/annotations/braker_wallacei_test/braker/GeneMark-ES
cd /data/selaginella/DATA/annotations/braker_wallacei_test/braker/GeneMark-ES
# Wed Jun 16 21:54:19 2021: Executing gmes_petap.pl
perl /data/selaginella/anaconda3/envs/braker2_conda_env/gmes_linux_64/gmes_petap.pl --verbose --cores=8 --ES --gc_donor 0.001 --sequence=/data/selaginella/DATA/annotations/braker_wallacei_test/braker/genome.fa --soft_mask auto 1>/data/selaginella/DATA/annotations/braker_wallacei_test/braker/GeneMark-ES.stdout 2>/data/selaginella/DATA/annotations/braker_wallacei_test/braker/errors/GeneMark-ES.stderr
# Wed Jun 16 22:42:10 2021: change to working directory /data/selaginella/DATA/annotations/braker_wallacei_test/braker
cd /data/selaginella/DATA/annotations/braker_wallacei_test/braker
# Wed Jun 16 22:42:10 2021: Calling prothint.py...
# Wed Jun 16 22:42:10 2021: starting prothint.py
/data/selaginella/anaconda3/envs/braker2_conda_env/ProtHint/bin/prothint.py --threads=8 --geneMarkGtf /data/selaginella/DATA/annotations/braker_wallacei_test/braker/GeneMark-ES/genemark.gtf /data/selaginella/DATA/annotations/braker_wallacei_test/braker/genome.fa /data/selaginella/DATA/annotations/braker_wallacei_test/braker/proteins.fa
# Wed Jun 16 23:19:07 2021: Appending hints from /data/selaginella/DATA/annotations/braker_wallacei_test/braker/prothint_augustus.gff to /data/selaginella/DATA/annotations/braker_wallacei_test/braker/hintsfile.gff
# Wed Jun 16 23:19:07 2021: Generating hints with ProtHint finished.
# Wed Jun 16 23:19:07 2021: Converting bam files to hints
# Wed Jun 16 23:19:07 2021: Checking bam headers
# Wed Jun 16 23:19:07 2021: create header file /data/selaginella/DATA/annotations/braker_wallacei_test/braker/wallacei_header.sam
/data/selaginella/anaconda3/envs/braker2_conda_env/bin/bamtools header -in /data/selaginella/DATA/annotations/braker_wallacei_test/wallacei.sorted.bam > /data/selaginella/DATA/annotations/braker_wallacei_test/braker/wallacei_header.sam
# Wed Jun 16 23:19:09 2021: Deleting SAM header file /data/selaginella/DATA/annotations/braker_wallacei_test/braker/wallacei_header.sam (will not be needed from here on)
# Wed Jun 16 23:19:09 2021: Deleting /data/selaginella/DATA/annotations/braker_wallacei_test/braker/wallacei_new_header.sam
# Wed Jun 16 23:19:09 2021: make hints from BAM file /data/selaginella/DATA/annotations/braker_wallacei_test/wallacei.sorted.bam
/data/selaginella/anaconda3/envs/braker2_conda_env/bin/../config/../bin/bam2hints --intronsonly --in=/data/selaginella/DATA/annotations/braker_wallacei_test/wallacei.sorted.bam --out=/data/selaginella/DATA/annotations/braker_wallacei_test/braker/bam2hints.temp.0.gff 1> /data/selaginella/DATA/annotations/braker_wallacei_test/braker/errors/bam2hints.0.stdout 2>/data/selaginella/DATA/annotations/braker_wallacei_test/braker/errors/bam2hints.0.stderr
# Wed Jun 16 23:19:30 2021: add hints from BAM file /data/selaginella/DATA/annotations/braker_wallacei_test/wallacei.sorted.bam to hints file
cat /data/selaginella/DATA/annotations/braker_wallacei_test/braker/bam2hints.temp.0.gff >>/data/selaginella/DATA/annotations/braker_wallacei_test/braker/hintsfile.temp.gff
# Wed Jun 16 23:19:30 2021: Checking for hints of src=C and with grp tags that should not be joined according to multiplicity
mv /data/selaginella/DATA/annotations/braker_wallacei_test/braker/tmp_no_merge_hints.gff /data/selaginella/DATA/annotations/braker_wallacei_test/braker/hintsfile.temp.gff
# Wed Jun 16 23:19:30 2021: filter introns, find strand and change score to 'mult' entry
perl /data/selaginella/anaconda3/envs/braker2_conda_env/BRAKER-2.1.6/scripts/filterIntronsFindStrand.pl /data/selaginella/DATA/annotations/braker_wallacei_test/braker/genome.fa /data/selaginella/DATA/annotations/braker_wallacei_test/braker/hintsfile.temp.gff --score 1>>/data/selaginella/DATA/annotations/braker_wallacei_test/braker/hintsfile.gff 2>/data/selaginella/DATA/annotations/braker_wallacei_test/braker/errors/filterIntronsFindStrand.stderr
# Wed Jun 16 23:19:31 2021: rm /data/selaginella/DATA/annotations/braker_wallacei_test/braker/hintsfile.temp.gff
# Wed Jun 16 23:19:31 2021: Preparing hints for running GeneMark
# Wed Jun 16 23:19:31 2021: Filtering intron hints for GeneMark from /data/selaginella/DATA/annotations/braker_wallacei_test/braker/hintsfile.gff...
cat /data/selaginella/DATA/annotations/braker_wallacei_test/braker/genemark_hintsfile.gff.prot | sort -n -k 4,4 | sort -s -n -k 5,5 | sort -s -k 3,3 | sort -s -k 1,1 | /data/selaginella/anaconda3/envs/braker2_conda_env/augustus-3.4.0/scripts/join_mult_hints.pl > /data/selaginella/DATA/annotations/braker_wallacei_test/braker/genemark_hintsfile.gff.prot.tmp
cat /data/selaginella/DATA/annotations/braker_wallacei_test/braker/genemark_hintsfile.gff.rnaseq.tmp /data/selaginella/DATA/annotations/braker_wallacei_test/braker/genemark_hintsfile.gff.prot.tmp > /data/selaginella/DATA/annotations/braker_wallacei_test/braker/genemark_hintsfile.gff
Thank you for your help.
