#********************************************************************************** # BRAKER CONFIGURATION #********************************************************************************** # BRAKER CALL: /opt/BRAKER/scripts/braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam # Mon Nov 13 14:05:59 2023: braker.pl version 3.0.5 # Mon Nov 13 14:05:59 2023: Only RNA-Seq input detected, BRAKER will be executed in ET mode (BRAKER1). # Mon Nov 13 14:05:59 2023: Configuring of BRAKER for using external tools... # Mon Nov 13 14:05:59 2023: Trying to set $AUGUSTUS_CONFIG_PATH... # Mon Nov 13 14:05:59 2023: Found environment variable $AUGUSTUS_CONFIG_PATH. # Mon Nov 13 14:05:59 2023: Checking /usr/share/augustus/config/ as potential path for $AUGUSTUS_CONFIG_PATH. # Mon Nov 13 14:05:59 2023: Success! Setting $AUGUSTUS_CONFIG_PATH to /usr/share/augustus/config/! # Mon Nov 13 14:05:59 2023: Trying to set $AUGUSTUS_BIN_PATH... # Mon Nov 13 14:05:59 2023: Found environment variable $AUGUSTUS_BIN_PATH. # Mon Nov 13 14:05:59 2023: Checking /usr/bin/ as potential path for $AUGUSTUS_BIN_PATH. # Mon Nov 13 14:05:59 2023: Success! Setting $AUGUSTUS_BIN_PATH to /usr/bin/! # Mon Nov 13 14:05:59 2023: Trying to set $AUGUSTUS_SCRIPTS_PATH... # Mon Nov 13 14:05:59 2023: Found environment variable $AUGUSTUS_SCRIPTS_PATH. # Mon Nov 13 14:05:59 2023: Checking /usr/share/augustus/scripts/ as potential path for $AUGUSTUS_SCRIPTS_PATH. # Mon Nov 13 14:05:59 2023: Success! Setting $AUGUSTUS_SCRIPTS_PATH to /usr/share/augustus/scripts/! # Mon Nov 13 14:05:59 2023: Trying to set $PYTHON3_PATH... # Mon Nov 13 14:05:59 2023: Did not find environment variable $PYTHON3_PATH. # Mon Nov 13 14:05:59 2023: Trying to guess PYTHON3_PATH from location of python3 executable that is available in your $PATH # Mon Nov 13 14:05:59 2023: Checking /opt/conda/bin as potential path for $PYTHON3_PATH. # Mon Nov 13 14:05:59 2023: Success! Setting $PYTHON3_PATH to /opt/conda/bin! # Mon Nov 13 14:05:59 2023: Trying to set $GENEMARK_PATH... # Mon Nov 13 14:05:59 2023: Found environment variable $GENEMARK_PATH. # Mon Nov 13 14:05:59 2023: Checking /opt/ETP/bin as potential path for $GENEMARK_PATH. #********* # WARNING: Couldn't find gmes_petap.pl in /opt/ETP/bin. Will not set $GENEMARK_PATH to /opt/ETP/bin! #********* # Mon Nov 13 14:05:59 2023: Trying to guess GENEMARK_PATH from location of gmes_petap.pl executable that is available in your $PATH # Mon Nov 13 14:05:59 2023: Checking /opt/ETP/bin/gmes as potential path for $GENEMARK_PATH. # Mon Nov 13 14:05:59 2023: Success! Setting $GENEMARK_PATH to /opt/ETP/bin/gmes! # Mon Nov 13 14:05:59 2023: Trying to set $BAMTOOLS_PATH... # Mon Nov 13 14:05:59 2023: Did not find environment variable $BAMTOOLS_PATH. # Mon Nov 13 14:05:59 2023: Trying to guess BAMTOOLS_PATH from location of bamtools executable that is available in your $PATH # Mon Nov 13 14:05:59 2023: Checking /usr/bin as potential path for $BAMTOOLS_PATH. # Mon Nov 13 14:05:59 2023: Success! Setting $BAMTOOLS_PATH to /usr/bin! # Mon Nov 13 14:05:59 2023: Trying to set $SAMTOOLS_PATH... # Mon Nov 13 14:05:59 2023: Did not find environment variable $SAMTOOLS_PATH. # Mon Nov 13 14:05:59 2023: Trying to guess SAMTOOLS_PATH from location of samtools executable that is available in your $PATH # Mon Nov 13 14:05:59 2023: Checking /usr/bin as potential path for $SAMTOOLS_PATH. # Mon Nov 13 14:05:59 2023: Success! Setting $SAMTOOLS_PATH to /usr/bin! # Mon Nov 13 14:05:59 2023: Trying to set $DIAMOND_PATH... # Mon Nov 13 14:05:59 2023: Did not find environment variable $DIAMOND_PATH. # Mon Nov 13 14:05:59 2023: Trying to guess DIAMOND_PATH from location of diamond executable that is available in your $PATH # Mon Nov 13 14:05:59 2023: Checking /opt/ETP/tools as potential path for $DIAMOND_PATH. # Mon Nov 13 14:05:59 2023: Success! Setting $DIAMOND_PATH to /opt/ETP/tools! # Mon Nov 13 14:05:59 2023: Trying to set $TSEBRA_PATH... # Mon Nov 13 14:05:59 2023: Did not find environment variable $TSEBRA_PATH. # Mon Nov 13 14:05:59 2023: Trying to guess TSEBRA_PATH from location of tsebra.py executable that is available in your $PATH # Mon Nov 13 14:05:59 2023: Checking /opt/TSEBRA/bin as potential path for $TSEBRA_PATH. # Mon Nov 13 14:05:59 2023: Success! Setting $TSEBRA_PATH to /opt/TSEBRA/bin! # Mon Nov 13 14:05:59 2023: Trying to set $CDBTOOLS_PATH... # Mon Nov 13 14:05:59 2023: Did not find environment variable $CDBTOOLS_PATH. # Mon Nov 13 14:05:59 2023: Trying to guess CDBTOOLS_PATH from location of cdbfasta executable that is available in your $PATH # Mon Nov 13 14:05:59 2023: Checking /opt/cdbfasta as potential path for $CDBTOOLS_PATH. # Mon Nov 13 14:05:59 2023: Success! Setting $CDBTOOLS_PATH to /opt/cdbfasta! #********************************************************************************** # CREATING DIRECTORY STRUCTURE #********************************************************************************** # Mon Nov 13 14:05:59 2023: creating file that contains citations for this BRAKER run at /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/what-to-cite.txt... # Mon Nov 13 14:05:59 2023: changing into working directory /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker cd /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker # Mon Nov 13 14:05:59 2023: getting GC content of the genome /opt/BRAKER/scripts/get_gc_content.py --sequences /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_2/parasite.fa.ref.fa --print_sequence_length 1> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/gc_content.out 2> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/gc_content.stderr # Mon Nov 13 14:06:01 2023: Creating parameter template files for AUGUSTUS with new_species.pl # Mon Nov 13 14:06:01 2023: new_species.pl will create parameter files for species run1 in /usr/share/augustus/config//species/run1 /usr/bin/perl /usr/share/augustus/scripts/new_species.pl --species=run1 --AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config/ 1> /dev/null 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/new_species.stderr # Mon Nov 13 14:06:01 2023: check_fasta_headers(): Checking fasta headers of file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_2/parasite.fa.ref.fa #********************************************************************************** # PROCESSING HINTS #********************************************************************************** # Mon Nov 13 14:06:01 2023: Converting bam files to hints # Mon Nov 13 14:06:01 2023: Checking bam headers # Mon Nov 13 14:06:01 2023: create header file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/S_l1_1_header.sam /usr/bin/bamtools header -in /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/S_l1_1.fq.bam > /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/S_l1_1_header.sam # Mon Nov 13 14:06:01 2023: Deleting SAM header file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/S_l1_1_header.sam (will not be needed from here on) # Mon Nov 13 14:06:01 2023: Deleting /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/S_l1_1_new_header.sam # Mon Nov 13 14:06:01 2023: make hints from BAM file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/S_l1_1.fq.bam /usr/bin//bam2hints --intronsonly --in=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/S_l1_1.fq.bam --out=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/bam2hints.temp.0.gff 1> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/bam2hints.0.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/bam2hints.0.stderr # Mon Nov 13 14:37:09 2023: add hints from BAM file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/S_l1_1.fq.bam to hints file cat /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/bam2hints.temp.0.gff >>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/hintsfile.temp.gff # Mon Nov 13 14:37:09 2023: Checking for hints of src=C and with grp tags that should not be joined according to multiplicity # Mon Nov 13 14:37:09 2023: Joining hints that are identical (& from the same source) into multiplicity hints (input file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/tmp_merge_hints.gff) # Mon Nov 13 14:37:09 2023: sort hints of type rnaseq cat /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/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 >/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/hints.rnaseq.temp.sort.gff # Mon Nov 13 14:37:09 2023: join multiple hints /usr/bin/perl /usr/share/augustus/scripts/join_mult_hints.pl /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/tmp_merge_hints.gff 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/join_mult_hints.rnaseq.stderr mv /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/tmp_merge_hints.gff /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/hintsfile.temp.gff # Mon Nov 13 14:37:09 2023: filter introns, find strand and change score to 'mult' entry /usr/bin/perl /opt/BRAKER/scripts/filterIntronsFindStrand.pl /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genome.fa /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/hintsfile.temp.gff --score 1>>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/hintsfile.gff 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/filterIntronsFindStrand.stderr # Mon Nov 13 14:37:09 2023: rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/hintsfile.temp.gff # Mon Nov 13 14:37:09 2023: Preparing hints for running GeneMark # Mon Nov 13 14:37:09 2023: Filtering intron hints for GeneMark from /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/hintsfile.gff... cat /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/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 | /usr/share/augustus/scripts/join_mult_hints.pl > /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genemark_hintsfile.gff.rnaseq.tmp mv /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genemark_hintsfile.gff.rnaseq.tmp /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genemark_hintsfile.gff #********************************************************************************** # RUNNING GENEMARK-EX #********************************************************************************** # Mon Nov 13 14:37:09 2023: Checking whether file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genemark_hintsfile.gff contains enough hints and sufficient multiplicity information... # Mon Nov 13 14:37:09 2023: Executing GeneMark-ET # Mon Nov 13 14:37:09 2023: changing into GeneMark-ET directory /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET cd /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET # Mon Nov 13 14:37:09 2023: Executing gmes_petap.pl /usr/bin/perl /opt/ETP/bin/gmes/gmes_petap.pl --verbose --sequence=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genome.fa --ET=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genemark_hintsfile.gff --cores=1 --gc_donor 0.001 --soft_mask auto 1>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/GeneMark-ET.stderr # Mon Nov 13 14:55:06 2023: change to working directory /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker cd /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker # Mon Nov 13 14:55:06 2023: Filtering output of GeneMark for generating training genes for AUGUSTUS # Mon Nov 13 14:55:06 2023: Checking whether hintsfile contains single exon CDSpart hints or start/stop hints # Mon Nov 13 14:55:06 2023: sorting GeneMark predictions in /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.gtf /opt/conda/bin/python3 /opt/BRAKER/scripts/sortGeneMark.py /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.gtf > /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.gtf.sorted 2> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/sortGeneMark.err mv /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.gtf.sorted /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.gtf # Mon Nov 13 14:55:07 2023: filtering GeneMark genes by intron hints /usr/bin/perl /opt/BRAKER/scripts/filterGenemark.pl --genemark=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.gtf --hints=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/hintsfile.gff --randomSeed=1 1>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/filterGenemark.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/filterGenemark.stderr # Mon Nov 13 14:55:07 2023: Ensuring at least 4000 genes in training file /opt/conda/bin/python3 /opt/BRAKER/scripts/ensure_n_training_genes.py --goodGenes /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.f.good.gtf --badGenes /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.f.bad.gtf --N 4000 1>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/ensure_min_n_training_genes.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/ensure_min_n_training_genes.stderr #Mon Nov 13 14:55:07 2023: downsampling good genemark genes according to poisson distribution with Lambda 2: /usr/bin/perl /opt/BRAKER/scripts/downsample_traingenes.pl --in_gtf=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.f.good.gtf --out_gtf=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.d.gtf --lambda=2 1> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/downsample_traingenes.log 2> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/downsample_traingenes.err #********************************************************************************** # TRAIN AUGUSTUS #********************************************************************************** # Mon Nov 13 14:55:07 2023: training AUGUSTUS # Mon Nov 13 14:55:07 2023: creating softlink from /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.gtf to /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/traingenes.gtf. ln -s /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.gtf /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/traingenes.gtf # Mon Nov 13 14:55:07 2023: Converting gtf file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/traingenes.gtf to genbank file # Mon Nov 13 14:55:07 2023: Computing flanking region size for AUGUSTUS training genes # Mon Nov 13 14:55:08 2023: create genbank file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb /usr/bin/perl /usr/share/augustus/scripts/gff2gbSmallDNA.pl /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/traingenes.gtf /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genome.fa 1084 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/traingenes.gtf_gff2gbSmallDNA.stderr #********* # INFORMATION: the size of flanking region used in this BRAKER run is 1084. You might need this value if you later add a UTR training on top of an already existing BRAKER run. #********* # Mon Nov 13 14:55:11 2023: Genbank format file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb contains 3666 genes. # Mon Nov 13 14:55:11 2023: concatenating good and downsampled GeneMark training genes to /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/good_genes.lst. cat /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.d.gtf > /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/good_genes.lst # Mon Nov 13 14:55:11 2023: Filtering train.gb for "good" mRNAs: /usr/bin/perl /usr/share/augustus/scripts/filterGenesIn_mRNAname.pl /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/good_genes.lst /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb > /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.f.gb 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/filterGenesIn_mRNAname.stderr # Mon Nov 13 14:55:11 2023: Genbank format file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.f.gb contains 2679 genes. # Mon Nov 13 14:55:11 2023: Running etraining to catch gene structure inconsistencies: /usr/bin//etraining --species=run1 --AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config/ /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.f.gb 1> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/gbFilterEtraining.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/gbFilterEtraining.stderr # Mon Nov 13 14:55:13 2023: Filtering /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.f.gb file to remove inconsistent gene structures... /usr/bin/perl /usr/share/augustus/scripts/filterGenes.pl /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/etrain.bad.lst /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.f.gb 1> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.ff.gb 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/etrainFilterGenes.stderr # Mon Nov 13 14:55:13 2023: Genbank format file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.ff.gb contains 2679 genes. # Mon Nov 13 14:55:15 2023: BLAST or DIAMOND training gene structures against themselves: /usr/bin/perl /usr/share/augustus/scripts/aa2nonred.pl /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/traingenes.good.fa /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/traingenes.good.nr.fa --DIAMOND_PATH=/opt/ETP/tools --cores=1 --diamond 1> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/aa2nonred.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/aa2nonred.stderr # Mon Nov 13 14:55:16 2023: Filtering nonredundant loci into /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.fff.gb: /usr/bin/perl /usr/share/augustus/scripts/filterGenesIn.pl /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/nonred.loci.lst /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.ff.gb 1> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.fff.gb 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/filterGenesIn.stderr # Mon Nov 13 14:55:16 2023: Genbank format file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.fff.gb contains 2678 genes. # Mon Nov 13 14:55:16 2023: Moving /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.fff.gb to /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb: mv /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.fff.gb /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb # Mon Nov 13 14:55:17 2023: Splitting genbank file into train and test file /usr/bin/perl /usr/share/augustus/scripts/randomSplit.pl /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb 300 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/randomSplit.stderr # Mon Nov 13 14:55:17 2023: /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.test will be used for measuring AUGUSTUS accuracy after training # Mon Nov 13 14:55:17 2023: Genbank format file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.test contains 300 genes. # Mon Nov 13 14:55:17 2023: Genbank format file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train contains 2378 genes. /usr/bin/perl /usr/share/augustus/scripts/randomSplit.pl /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train 300 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/randomSplit.stderr # Mon Nov 13 14:55:18 2023: Genbank format file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train.train contains 2078 genes. # Mon Nov 13 14:55:18 2023: Genbank format file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train.test contains 300 genes. # Mon Nov 13 14:55:18 2023: /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train.test will be used or measuring AUGUSTUS accuracy during training with optimize_augustus.pl /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train.train will be used for running etraining in optimize_augustus.pl (together with train.gb.train.test) /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train will be used for running etraining (outside of optimize_augustus.pl) # Mon Nov 13 14:55:18 2023: Setting value of "stopCodonExcludedFromCDS" in /usr/share/augustus/config//species/run1/run1_parameters.cfg to "true" # Mon Nov 13 14:55:18 2023: first etraining /usr/bin//etraining --species=run1 --AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config/ /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train 1>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/firstetraining.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/firstetraining.stderr grep -c "exon doesn't end in stop codon" /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/firstetraining.stderr # Mon Nov 13 14:55:20 2023: Error rate of missing stop codon is 0.927670311185871 # Mon Nov 13 14:55:20 2023: The appropriate value for "stopCodonExcludedFromCDS" seems to be "false". # Mon Nov 13 14:55:20 2023: Setting value of "stopCodonExcludedFromCDS" in /usr/share/augustus/config//species/run1/run1_parameters.cfg to "false" # Mon Nov 13 14:55:20 2023: Running etraining again /usr/bin//etraining --species=run1 --AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config/ /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train 1>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/firstetraining.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/firstetraining.stderr # Mon Nov 13 14:55:23 2023: Adjusting stop-codon frequencies in species_parameters.cfg according to /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/firstetraining.stdout # Mon Nov 13 14:55:23 2023: Setting frequency of stop codons to tag=0.21, taa=0.447, tga=0.343. # Mon Nov 13 14:55:23 2023: First AUGUSTUS accuracy test /usr/bin//augustus --species=run1 --AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config/ /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.test 1>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/firsttest.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/firsttest.stderr # Mon Nov 13 14:56:04 2023: Computing accuracy of AUGUSTUS prediction (in test file derived from predictions on training data set stored in /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/firsttest.stdout) # Mon Nov 13 14:56:04 2023: The accuracy after initial training (no optimize_augustus.pl, no CRF) is 0.5438 # Mon Nov 13 14:56:04 2023: optimizing AUGUSTUS parameters /usr/bin/perl /usr/share/augustus/scripts/optimize_augustus.pl --aug_exec_dir=/usr/bin/ --rounds=5 --species=run1 --kfold=8 --AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config/ --onlytrain=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train.train /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train.test 1>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/optimize_augustus.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/optimize_augustus.stderr # Tue Nov 14 00:59:54 2023: parameter optimization finished. # Tue Nov 14 00:59:54 2023: Second etraining /usr/bin//etraining --species=run1 --AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config/ /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train 1>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/secondetraining.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/secondetraining.stderr # Tue Nov 14 00:59:55 2023: Second AUGUSTUS accuracy test /usr/bin//augustus --species=run1 --AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config/ /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.test >/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/secondtest.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/secondtest.stderr # Tue Nov 14 01:00:35 2023: Computing accuracy of AUGUSTUS prediction (in test file derived from predictions on training data set stored in /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/secondtest.stdout) # Tue Nov 14 01:00:35 2023: The accuracy after training (after optimize_augustus.pl, no CRF) is 0.785666666666667 # Tue Nov 14 01:00:35 2023: Copying optimized parameters to working directory /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/species cp -r /usr/share/augustus/config//species/run1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/species #********************************************************************************** # PREDICTING GENES WITH AUGUSTUS (NO UTRS) #********************************************************************************** # Tue Nov 14 01:00:35 2023: RUNNING AUGUSTUS # Tue Nov 14 01:00:35 2023: copy extrinsic file /opt/BRAKER/scripts/cfg/rnaseq.cfg to working directory cp /opt/BRAKER/scripts/cfg/rnaseq.cfg /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/species/run1/ex1.cfg # Tue Nov 14 01:00:35 2023: Running AUGUSTUS with hints for file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genome.fa /usr/bin//augustus --species=run1 --AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config/ --extrinsicCfgFile=/opt/BRAKER/scripts/cfg/rnaseq.cfg --alternatives-from-evidence=true --hintsfile=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/hintsfile.gff --UTR=off --exonnames=on --codingseq=on --allow_hinted_splicesites=gcag,atac --softmasking=1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genome.fa 1>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.gff 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/augustus.hints.stderr # Tue Nov 14 01:18:49 2023: Making a gtf file from /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.gff cat /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.gff | /usr/bin/perl -ne 'if(m/\tAUGUSTUS\t/) {print $_;}' | /usr/bin/perl /usr/share/augustus/scripts/gtf2gff.pl --printExon --out=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.tmp.gtf 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/gtf2gff.augustus.hints.gtf.stderr # Tue Nov 14 01:18:50 2023: Making a fasta file with protein sequences of /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.gtf /opt/conda/bin/python3 /usr/share/augustus/scripts/getAnnoFastaFromJoingenes.py -g /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genome.fa -f /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.gtf -o /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints 1> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/getAnnoFastaFromJoingenes.augustus.hints_tmp.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/getAnnoFastaFromJoingenes.augustus.hints_tmp.stderr # Tue Nov 14 01:18:54 2023: fixing AUGUSTUS genes with in frame stop codons... /opt/conda/bin/python3 /usr/share/augustus/scripts/fix_in_frame_stop_codon_genes.py -g /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genome.fa -t /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.gtf -b /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/bad_genes.lst -o augustus.hints_fix_ifs_ -s run1 -m on --UTR off --print_utr off -a /usr/share/augustus/config/ -C /opt/cdbfasta -A /usr/bin/ -S /usr/share/augustus/scripts/ -H /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/hintsfile.gff -e /opt/BRAKER/scripts/cfg/rnaseq.cfg > /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/fix_in_frame_stop_codon_genes_augustus.hints.log 2> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/fix_in_frame_stop_codon_genes_augustus.hints.err # Tue Nov 14 01:19:03 2023: Moving gene prediction file without in frame stop codons to location of original file (overwriting it)... mv /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints_fix_ifs_.gtf /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.gtf # Tue Nov 14 01:19:04 2023: Deleting file with genes with in frame stop codons... rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/bad_genes.lst # Tue Nov 14 01:19:04 2023: Making a fasta file with protein sequences of /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.gtf /opt/conda/bin/python3 /usr/share/augustus/scripts/getAnnoFastaFromJoingenes.py -g /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genome.fa -f /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.gtf -o /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints 1> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/getAnnoFastaFromJoingenes.augustus.hints_hints.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/getAnnoFastaFromJoingenes.augustus.hints_hints.stderr # Tue Nov 14 01:19:06 2023: AUGUSTUS prediction complete # Tue Nov 14 01:19:06 2023: Trying to create merged gene set from GeneMark-EX and AUGUSTUS predictions (braker.gtf/braker.utr.gtf)... # Tue Nov 14 01:19:06 2023: Trying to create combined gene set with TSEBRA... /opt/TSEBRA/bin/tsebra.py --keep_gtf /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.gtf,/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.f.multi_anchored.gtf,/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.f.single_anchored.gtf --cfg /opt/TSEBRA/bin/../config/braker3.cfg --out /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/braker.gtf -q 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/tsebra.stderr mv /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/braker.gtf /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/braker.gtf_temp # Tue Nov 14 01:19:08 2023: Making a fasta file with protein sequences of /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/braker.gtf /opt/conda/bin/python3 /usr/share/augustus/scripts/getAnnoFastaFromJoingenes.py -g /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genome.fa -f /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/braker.gtf -o /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/braker 1> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/getAnnoFastaFromJoingenes.braker_.stdout 2>/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/getAnnoFastaFromJoingenes.braker_.stderr # Tue Nov 14 01:19:10 2023: deleting empty files # Tue Nov 14 01:19:10 2023: find /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker -empty rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/fix_in_frame_stop_codon_genes_augustus.hints.log rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/tmp_no_merge_hints.gff rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/ensure_min_n_training_genes.stdout rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/etrain.bad.lst rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/downsample_traingenes.log rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.f.single_anchored.gtf rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/data/plus.gff rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/data/in_mask.gff rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.f.bad.gtf rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/singlecds.hints rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/getAnnoFastaFromJoingenes.braker_.stdout rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/getAnnoFastaFromJoingenes.augustus.hints_hints.stdout rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/getAnnoFastaFromJoingenes.braker_.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/getAnnoFastaFromJoingenes.augustus.hints_tmp.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/bam2hints.0.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/find_python3_re.err rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/filterGenesIn_mRNAname.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/new_species.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/gtf2gff.augustus.hints.gtf.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/filterIntronsFindStrand.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/traingenes.gtf_gff2gbSmallDNA.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/downsample_traingenes.err rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/etrainFilterGenes.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/tsebra_rename.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/secondetraining.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/gc_content.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/firstetraining.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/optimize_augustus.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/filterGenemark.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/join_mult_hints.rnaseq.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/bam2hints.0.stdout rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/tsebra.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/filterGenesIn.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/getAnnoFastaFromJoingenes.augustus.hints_hints.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/firsttest.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/GeneMark-ET.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/find_python3_biopython.err rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/randomSplit.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/fix_in_frame_stop_codon_genes_augustus.hints.err rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/secondtest.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/augustus.hints.stderr rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/sortGeneMark.err rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/errors/gbFilterEtraining.stderr # Tue Nov 14 01:19:10 2023: deleting job lst files (if existing) rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/fix_IFS_log_gjwgxekj rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.tmp.gtf rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.test rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/firstetraining.stdout rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train.test rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.ff.gb rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/traingenes.good.nr.fa rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/aa2nonred.stdout rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/secondetraining.stdout rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/good_genes.lst rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/traingenes.gtf rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/nonred.loci.lst rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train.train rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb.train rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/traingenes.good.fa rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/gbFilterEtraining.stdout rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/traingenes.good.gtf rm /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.f.gb /usr/bin/perl /opt/BRAKER/scripts/braker_cleanup.pl --wdir=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/firsttest.stdout Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genome.fa Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/optimize_augustus.stdout Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/secondtest.stdout Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/train.gb Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.d.gtf Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.f.good.gtf Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.c.gtf Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/genemark.average_gene_length.out Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/gmes.log Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/run.cfg Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET.stdout Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/filterGenemark.stdout Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genome.fa.cidx Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/getAnnoFastaFromJoingenes.augustus.hints_tmp.stdout Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/augustus.hints.gff Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/braker.gtf_temp Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/genemark_hintsfile.gff Deleting file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/gc_content.out Deleting directory /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/data Deleting directory /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/info Deleting directory /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/output Deleting directory /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/GeneMark-ET/run #********************************************************************************** # BRAKER RUN FINISHED #**********************************************************************************