#********************************************************************************** # BRAKER CONFIGURATION #********************************************************************************** # BRAKER CALL: /root/BRAKER/scripts/braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam # Sat Jan 16 07:19:16 2021: braker.pl version 2.1.5 # Sat Jan 16 07:19:16 2021: Configuring of BRAKER for using external tools... # Sat Jan 16 07:19:16 2021: Found environment variable $AUGUSTUS_CONFIG_PATH. Setting $AUGUSTUS_CONFIG_PATH to /yoshitake/test/annotation~BRAKER2/config/ # Sat Jan 16 07:19:16 2021: Found environment variable $AUGUSTUS_BIN_PATH. Setting $AUGUSTUS_BIN_PATH to /root/Augustus/bin # Sat Jan 16 07:19:16 2021: Found environment variable $AUGUSTUS_SCRIPTS_PATH. Setting $AUGUSTUS_SCRIPTS_PATH to /root/Augustus/scripts # Sat Jan 16 07:19:16 2021: Did not find environment variable $PYTHON3_PATH # Sat Jan 16 07:19:16 2021: Trying to guess $PYTHON3_PATH from location of python3 executable that is available in your $PATH # Sat Jan 16 07:19:16 2021: Setting $PYTHON3_PATH to /root/anaconda3/bin # Sat Jan 16 07:19:16 2021: Found environment variable $GENEMARK_PATH. Setting $GENEMARK_PATH to /yoshitake/test/annotation~BRAKER2/gmes_linux_64 # Sat Jan 16 07:19:16 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. # Sat Jan 16 07:19:16 2021: Trying to guess $BAMTOOLS_BIN_PATH from location of bamtools executable that is available in your $PATH # Sat Jan 16 07:19:16 2021: Setting $BAMTOOLS_BIN_PATH to /root/anaconda3/bin # Sat Jan 16 07:19:16 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. # Sat Jan 16 07:19:16 2021: Trying to guess $SAMTOOLS_PATH from location of samtools executable in your $PATH # Sat Jan 16 07:19:16 2021: Setting $SAMTOOLS_PATH to /root/anaconda3/bin # Sat Jan 16 07:19:16 2021: Did not find environment variable $DIAMOND_PATH # Sat Jan 16 07:19:16 2021: Trying to guess $DIAMOND_PATH from location of diamond executable that is available in your $PATH # Sat Jan 16 07:19:16 2021: Setting $DIAMOND_PATH to /usr/local/bin # Sat Jan 16 07:19:16 2021: Did not find environment variable $CDBTOOLS_PATH # Sat Jan 16 07:19:16 2021: Trying to guess $CDBTOOLS_PATH from location of cdbfasta executable that is available in your $PATH # Sat Jan 16 07:19:16 2021: Setting $CDBTOOLS_PATH to /usr/bin #********************************************************************************** # CREATING DIRECTORY STRUCTURE #********************************************************************************** # Sat Jan 16 07:19:16 2021: create working directory /yoshitake/test/annotation~BRAKER2/braker. mkdir /yoshitake/test/annotation~BRAKER2/braker # Sat Jan 16 07:19:16 2021: creating file that contains citations for this BRAKER run at /yoshitake/test/annotation~BRAKER2/braker/what-to-cite.txt... # Sat Jan 16 07:19:16 2021: create working directory /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET. mkdir /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET # Sat Jan 16 07:19:16 2021: create working directory /yoshitake/test/annotation~BRAKER2/braker/species mkdir /yoshitake/test/annotation~BRAKER2/braker/species # Sat Jan 16 07:19:16 2021: create working directory /yoshitake/test/annotation~BRAKER2/braker/errors mkdir /yoshitake/test/annotation~BRAKER2/braker/errors # Sat Jan 16 07:19:16 2021: changing into working directory /yoshitake/test/annotation~BRAKER2/braker cd /yoshitake/test/annotation~BRAKER2/braker # Sat Jan 16 07:19:16 2021: Creating parameter template files for AUGUSTUS with new_species.pl # Sat Jan 16 07:19:16 2021: new_species.pl will create parameter files for species run1 in /yoshitake/test/annotation~BRAKER2/config//species/run1 perl /root/Augustus/scripts/new_species.pl --species=run1 --AUGUSTUS_CONFIG_PATH=/yoshitake/test/annotation~BRAKER2/config/ 1> /dev/null 2>/yoshitake/test/annotation~BRAKER2/braker/errors/new_species.stderr # Sat Jan 16 07:19:16 2021: check_fasta_headers(): Checking fasta headers of file /yoshitake/test/annotation~BRAKER2/input_2/parasite.fa.ref.fa #********************************************************************************** # PROCESSING HINTS #********************************************************************************** # Sat Jan 16 07:19:16 2021: Converting bam files to hints # Sat Jan 16 07:19:16 2021: Checking bam headers # Sat Jan 16 07:19:16 2021: create header file /yoshitake/test/annotation~BRAKER2/braker/S_l1_1_header.sam /root/anaconda3/bin/bamtools header -in /yoshitake/test/annotation~BRAKER2/S_l1_1.fq.bam > /yoshitake/test/annotation~BRAKER2/braker/S_l1_1_header.sam # Sat Jan 16 07:19:16 2021: Deleting SAM header file /yoshitake/test/annotation~BRAKER2/braker/S_l1_1_header.sam (will not be needed from here on) # Sat Jan 16 07:19:16 2021: Deleting /yoshitake/test/annotation~BRAKER2/braker/S_l1_1_new_header.sam # Sat Jan 16 07:19:16 2021: make hints from BAM file /yoshitake/test/annotation~BRAKER2/S_l1_1.fq.bam /root/Augustus/bin/bam2hints --intronsonly --in=/yoshitake/test/annotation~BRAKER2/S_l1_1.fq.bam --out=/yoshitake/test/annotation~BRAKER2/braker/bam2hints.temp.0.gff 1> /yoshitake/test/annotation~BRAKER2/braker/errors/bam2hints.0.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/bam2hints.0.stderr # Sat Jan 16 07:32:48 2021: add hints from BAM file /yoshitake/test/annotation~BRAKER2/S_l1_1.fq.bam to hints file cat /yoshitake/test/annotation~BRAKER2/braker/bam2hints.temp.0.gff >>/yoshitake/test/annotation~BRAKER2/braker/hintsfile.temp.gff # Sat Jan 16 07:32:48 2021: Checking for hints of src=C and with grp tags that should not be joined according to multiplicity # Sat Jan 16 07:32:48 2021: Joining hints that are identical (& from the same source) into multiplicity hints (input file /yoshitake/test/annotation~BRAKER2/braker/tmp_merge_hints.gff) # Sat Jan 16 07:32:48 2021: sort hints of type rnaseq cat /yoshitake/test/annotation~BRAKER2/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 >/yoshitake/test/annotation~BRAKER2/braker/hints.rnaseq.temp.sort.gff # Sat Jan 16 07:32:48 2021: join multiple hints perl /root/Augustus/scripts/join_mult_hints.pl /yoshitake/test/annotation~BRAKER2/braker/tmp_merge_hints.gff 2>/yoshitake/test/annotation~BRAKER2/braker/errors/join_mult_hints.rnaseq.stderr mv /yoshitake/test/annotation~BRAKER2/braker/tmp_merge_hints.gff /yoshitake/test/annotation~BRAKER2/braker/hintsfile.temp.gff # Sat Jan 16 07:32:48 2021: filter introns, find strand and change score to 'mult' entry perl /root/BRAKER/scripts/filterIntronsFindStrand.pl /yoshitake/test/annotation~BRAKER2/braker/genome.fa /yoshitake/test/annotation~BRAKER2/braker/hintsfile.temp.gff --score 1>>/yoshitake/test/annotation~BRAKER2/braker/hintsfile.gff 2>/yoshitake/test/annotation~BRAKER2/braker/errors/filterIntronsFindStrand.stderr # Sat Jan 16 07:32:48 2021: rm /yoshitake/test/annotation~BRAKER2/braker/hintsfile.temp.gff # Sat Jan 16 07:32:48 2021: Preparing hints for running GeneMark # Sat Jan 16 07:32:48 2021: Filtering intron hints for GeneMark from /yoshitake/test/annotation~BRAKER2/braker/hintsfile.gff... cat /yoshitake/test/annotation~BRAKER2/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 | /root/Augustus/scripts/join_mult_hints.pl > /yoshitake/test/annotation~BRAKER2/braker/genemark_hintsfile.gff.rnaseq.tmp mv /yoshitake/test/annotation~BRAKER2/braker/genemark_hintsfile.gff.rnaseq.tmp /yoshitake/test/annotation~BRAKER2/braker/genemark_hintsfile.gff #********************************************************************************** # RUNNING GENEMARK-EX #********************************************************************************** # Sat Jan 16 07:32:48 2021: Checking whether file /yoshitake/test/annotation~BRAKER2/braker/genemark_hintsfile.gff contains enough hints and sufficient multiplicity information... # Sat Jan 16 07:32:48 2021: Executing GeneMark-ET # Sat Jan 16 07:32:48 2021: changing into GeneMark-ET directory /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET cd /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET # Sat Jan 16 07:32:48 2021: Executing gmes_petap.pl perl /yoshitake/test/annotation~BRAKER2/gmes_linux_64/gmes_petap.pl --verbose --sequence=/yoshitake/test/annotation~BRAKER2/braker/genome.fa --ET=/yoshitake/test/annotation~BRAKER2/braker/genemark_hintsfile.gff --cores=1 --gc_donor 0.001 1>/yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/GeneMark-ET.stderr # Sat Jan 16 07:51:30 2021: change to working directory /yoshitake/test/annotation~BRAKER2/braker cd /yoshitake/test/annotation~BRAKER2/braker # Sat Jan 16 07:51:30 2021: Filtering output of GeneMark for generating training genes for AUGUSTUS # Sat Jan 16 07:51:30 2021: Checking whether hintsfile contains single exon CDSpart hints or start/stop hints # Sat Jan 16 07:51:30 2021: filtering GeneMark genes by intron hints perl /root/BRAKER/scripts/filterGenemark.pl --genemark=/yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.gtf --hints=/yoshitake/test/annotation~BRAKER2/braker/hintsfile.gff --randomSeed=1 1>/yoshitake/test/annotation~BRAKER2/braker/filterGenemark.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/filterGenemark.stderr # Sat Jan 16 07:51:31 2021: Ensuring at least 4000 genes in training file /root/anaconda3/bin/python3 /root/BRAKER/scripts/ensure_n_training_genes.py --goodGenes /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.f.good.gtf --badGenes /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.f.bad.gtf --N 4000 1>/yoshitake/test/annotation~BRAKER2/braker/ensure_min_n_training_genes.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/ensure_min_n_training_genes.stderr #Sat Jan 16 07:51:31 2021: downsampling good genemark genes according to poisson distribution with Lambda 2: perl /root/BRAKER/scripts/downsample_traingenes.pl --in_gtf=/yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.f.good.gtf --out_gtf=/yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.d.gtf --lambda=2 1> /yoshitake/test/annotation~BRAKER2/braker/downsample_traingenes.log 2> /yoshitake/test/annotation~BRAKER2/braker/errors/downsample_traingenes.err #********************************************************************************** # TRAIN AUGUSTUS #********************************************************************************** # Sat Jan 16 07:51:31 2021: training AUGUSTUS # Sat Jan 16 07:51:31 2021: creating softlink from /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.gtf to /yoshitake/test/annotation~BRAKER2/braker/traingenes.gtf. ln -s /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.gtf /yoshitake/test/annotation~BRAKER2/braker/traingenes.gtf # Sat Jan 16 07:51:31 2021: Converting gtf file /yoshitake/test/annotation~BRAKER2/braker/traingenes.gtf to genbank file # Sat Jan 16 07:51:31 2021: Computing flanking region size for AUGUSTUS training genes # Sat Jan 16 07:51:31 2021: create genbank file /yoshitake/test/annotation~BRAKER2/braker/train.gb perl /root/Augustus/scripts/gff2gbSmallDNA.pl /yoshitake/test/annotation~BRAKER2/braker/traingenes.gtf /yoshitake/test/annotation~BRAKER2/braker/genome.fa 1076 /yoshitake/test/annotation~BRAKER2/braker/train.gb 2>/yoshitake/test/annotation~BRAKER2/braker/errors/traingenes.gtf_gff2gbSmallDNA.stderr #********* # INFORMATION: the size of flanking region used in this BRAKER run is 1076. You might need this value if you later add a UTR training on top of an already existing BRAKER run. #********* # Sat Jan 16 07:51:34 2021: Genbank format file /yoshitake/test/annotation~BRAKER2/braker/train.gb contains 3657 genes. # Sat Jan 16 07:51:34 2021: concatenating good and downsampled GeneMark training genes to /yoshitake/test/annotation~BRAKER2/braker/good_genes.lst. cat /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.d.gtf > /yoshitake/test/annotation~BRAKER2/braker/good_genes.lst # Sat Jan 16 07:51:34 2021: Filtering train.gb for "good" mRNAs: perl /root/Augustus/scripts/filterGenesIn_mRNAname.pl /yoshitake/test/annotation~BRAKER2/braker/good_genes.lst /yoshitake/test/annotation~BRAKER2/braker/train.gb > /yoshitake/test/annotation~BRAKER2/braker/train.f.gb 2>/yoshitake/test/annotation~BRAKER2/braker/errors/filterGenesIn_mRNAname.stderr # Sat Jan 16 07:51:35 2021: Genbank format file /yoshitake/test/annotation~BRAKER2/braker/train.f.gb contains 2670 genes. # Sat Jan 16 07:51:35 2021: Running etraining to catch gene structure inconsistencies: /root/Augustus/bin/etraining --species=run1 --AUGUSTUS_CONFIG_PATH=/yoshitake/test/annotation~BRAKER2/config/ /yoshitake/test/annotation~BRAKER2/braker/train.f.gb 1> /yoshitake/test/annotation~BRAKER2/braker/gbFilterEtraining.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/gbFilterEtraining.stderr # Sat Jan 16 07:51:36 2021: Filtering /yoshitake/test/annotation~BRAKER2/braker/train.f.gb file to remove inconsistent gene structures... perl /root/Augustus/scripts/filterGenes.pl /yoshitake/test/annotation~BRAKER2/braker/etrain.bad.lst /yoshitake/test/annotation~BRAKER2/braker/train.f.gb 1> /yoshitake/test/annotation~BRAKER2/braker/train.ff.gb 2>/yoshitake/test/annotation~BRAKER2/braker/errors/etrainFilterGenes.stderr # Sat Jan 16 07:51:36 2021: Genbank format file /yoshitake/test/annotation~BRAKER2/braker/train.ff.gb contains 2072 genes. # Sat Jan 16 07:51:37 2021: BLAST or DIAMOND training gene structures against themselves: perl /root/Augustus/scripts/aa2nonred.pl /yoshitake/test/annotation~BRAKER2/braker/traingenes.good.fa /yoshitake/test/annotation~BRAKER2/braker/traingenes.good.nr.fa --DIAMOND_PATH=/usr/local/bin --cores=1 --diamond 1> /yoshitake/test/annotation~BRAKER2/braker/aa2nonred.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/aa2nonred.stderr # Sat Jan 16 07:51:39 2021: Filtering nonredundant loci into /yoshitake/test/annotation~BRAKER2/braker/train.fff.gb: perl /root/Augustus/scripts/filterGenesIn.pl /yoshitake/test/annotation~BRAKER2/braker/nonred.loci.lst /yoshitake/test/annotation~BRAKER2/braker/train.ff.gb 1> /yoshitake/test/annotation~BRAKER2/braker/train.fff.gb 2>/yoshitake/test/annotation~BRAKER2/braker/errors/filterGenesIn.stderr # Sat Jan 16 07:51:39 2021: Genbank format file /yoshitake/test/annotation~BRAKER2/braker/train.fff.gb contains 2072 genes. # Sat Jan 16 07:51:39 2021: Moving /yoshitake/test/annotation~BRAKER2/braker/train.fff.gb to /yoshitake/test/annotation~BRAKER2/braker/train.gb: mv /yoshitake/test/annotation~BRAKER2/braker/train.fff.gb /yoshitake/test/annotation~BRAKER2/braker/train.gb # Sat Jan 16 07:51:39 2021: Splitting genbank file into train and test file perl /root/Augustus/scripts/randomSplit.pl /yoshitake/test/annotation~BRAKER2/braker/train.gb 300 2>/yoshitake/test/annotation~BRAKER2/braker/errors/randomSplit.stderr # Sat Jan 16 07:51:39 2021: /yoshitake/test/annotation~BRAKER2/braker/train.gb.test will be used for measuring AUGUSTUS accuracy after training # Sat Jan 16 07:51:39 2021: Genbank format file /yoshitake/test/annotation~BRAKER2/braker/train.gb.test contains 300 genes. # Sat Jan 16 07:51:39 2021: Genbank format file /yoshitake/test/annotation~BRAKER2/braker/train.gb.train contains 1772 genes. perl /root/Augustus/scripts/randomSplit.pl /yoshitake/test/annotation~BRAKER2/braker/train.gb.train 300 2>/yoshitake/test/annotation~BRAKER2/braker/errors/randomSplit.stderr # Sat Jan 16 07:51:40 2021: Genbank format file /yoshitake/test/annotation~BRAKER2/braker/train.gb.train.train contains 1472 genes. # Sat Jan 16 07:51:40 2021: Genbank format file /yoshitake/test/annotation~BRAKER2/braker/train.gb.train.test contains 300 genes. # Sat Jan 16 07:51:40 2021: /yoshitake/test/annotation~BRAKER2/braker/train.gb.train.test will be used or measuring AUGUSTUS accuracy during training with optimize_augustus.pl /yoshitake/test/annotation~BRAKER2/braker/train.gb.train.train will be used for running etraining in optimize_augustus.pl (together with train.gb.train.test) /yoshitake/test/annotation~BRAKER2/braker/train.gb.train will be used for running etraining (outside of optimize_augustus.pl) # Sat Jan 16 07:51:40 2021: Setting value of "stopCodonExcludedFromCDS" in /yoshitake/test/annotation~BRAKER2/config//species/run1/run1_parameters.cfg to "true" # Sat Jan 16 07:51:40 2021: first etraining /root/Augustus/bin/etraining --species=run1 --AUGUSTUS_CONFIG_PATH=/yoshitake/test/annotation~BRAKER2/config/ /yoshitake/test/annotation~BRAKER2/braker/train.gb.train 1>/yoshitake/test/annotation~BRAKER2/braker/firstetraining.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/firstetraining.stderr grep -c "exon doesn't end in stop codon" /yoshitake/test/annotation~BRAKER2/braker/errors/firstetraining.stderr # Sat Jan 16 07:51:41 2021: Error rate of missing stop codon is 0.926636568848758 # Sat Jan 16 07:51:41 2021: The appropriate value for "stopCodonExcludedFromCDS" seems to be "false". # Sat Jan 16 07:51:41 2021: Setting value of "stopCodonExcludedFromCDS" in /yoshitake/test/annotation~BRAKER2/config//species/run1/run1_parameters.cfg to "false" # Sat Jan 16 07:51:41 2021: Running etraining again /root/Augustus/bin/etraining --species=run1 --AUGUSTUS_CONFIG_PATH=/yoshitake/test/annotation~BRAKER2/config/ /yoshitake/test/annotation~BRAKER2/braker/train.gb.train 1>/yoshitake/test/annotation~BRAKER2/braker/firstetraining.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/firstetraining.stderr # Sat Jan 16 07:51:42 2021: Adjusting stop-codon frequencies in species_parameters.cfg according to /yoshitake/test/annotation~BRAKER2/braker/firstetraining.stdout # Sat Jan 16 07:51:42 2021: Setting frequency of stop codons to tag=0.226, taa=0.425, tga=0.349. # Sat Jan 16 07:51:42 2021: First AUGUSTUS accuracy test /root/Augustus/bin/augustus --species=run1 --AUGUSTUS_CONFIG_PATH=/yoshitake/test/annotation~BRAKER2/config/ /yoshitake/test/annotation~BRAKER2/braker/train.gb.test 1>/yoshitake/test/annotation~BRAKER2/braker/firsttest.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/firsttest.stderr # Sat Jan 16 07:52:21 2021: Computing accuracy of AUGUSTUS prediction (in test file derived from predictions on training data set stored in /yoshitake/test/annotation~BRAKER2/braker/firsttest.stdout) # Sat Jan 16 07:52:21 2021: The accuracy after initial training (no optimize_augustus.pl, no CRF) is 0.55014 # Sat Jan 16 07:52:21 2021: optimizing AUGUSTUS parameters perl /root/Augustus/scripts/optimize_augustus.pl --aug_exec_dir=/root/Augustus/bin --rounds=5 --species=run1 --kfold=8 --AUGUSTUS_CONFIG_PATH=/yoshitake/test/annotation~BRAKER2/config/ --onlytrain=/yoshitake/test/annotation~BRAKER2/braker/train.gb.train.train /yoshitake/test/annotation~BRAKER2/braker/train.gb.train.test 1>/yoshitake/test/annotation~BRAKER2/braker/optimize_augustus.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/optimize_augustus.stderr # Sat Jan 16 14:01:10 2021: parameter optimization finished. # Sat Jan 16 14:01:10 2021: Second etraining /root/Augustus/bin/etraining --species=run1 --AUGUSTUS_CONFIG_PATH=/yoshitake/test/annotation~BRAKER2/config/ /yoshitake/test/annotation~BRAKER2/braker/train.gb.train 1>/yoshitake/test/annotation~BRAKER2/braker/secondetraining.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/secondetraining.stderr # Sat Jan 16 14:01:10 2021: Second AUGUSTUS accuracy test /root/Augustus/bin/augustus --species=run1 --AUGUSTUS_CONFIG_PATH=/yoshitake/test/annotation~BRAKER2/config/ /yoshitake/test/annotation~BRAKER2/braker/train.gb.test >/yoshitake/test/annotation~BRAKER2/braker/secondtest.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/secondtest.stderr # Sat Jan 16 14:01:41 2021: Computing accuracy of AUGUSTUS prediction (in test file derived from predictions on training data set stored in /yoshitake/test/annotation~BRAKER2/braker/secondtest.stdout) # Sat Jan 16 14:01:41 2021: The accuracy after training (after optimize_augustus.pl, no CRF) is 0.756666666666667 # Sat Jan 16 14:01:41 2021: Copying optimized parameters to working directory /yoshitake/test/annotation~BRAKER2/braker/species cp -r /yoshitake/test/annotation~BRAKER2/config//species/run1 /yoshitake/test/annotation~BRAKER2/braker/species #********************************************************************************** # PREDICTING GENES WITH AUGUSTUS (NO UTRS) #********************************************************************************** # Sat Jan 16 14:01:41 2021: RUNNING AUGUSTUS # Sat Jan 16 14:01:41 2021: copy extrinsic file /root/BRAKER/scripts/cfg/rnaseq.cfg to working directory cp /root/BRAKER/scripts/cfg/rnaseq.cfg /yoshitake/test/annotation~BRAKER2/braker/species/run1/ex1.cfg # Sat Jan 16 14:01:41 2021: Running AUGUSTUS with hints for file /yoshitake/test/annotation~BRAKER2/braker/genome.fa /root/Augustus/bin/augustus --species=run1 --AUGUSTUS_CONFIG_PATH=/yoshitake/test/annotation~BRAKER2/config/ --extrinsicCfgFile=/root/BRAKER/scripts/cfg/rnaseq.cfg --alternatives-from-evidence=true --hintsfile=/yoshitake/test/annotation~BRAKER2/braker/hintsfile.gff --UTR=off --exonnames=on --codingseq=on --allow_hinted_splicesites=gcag,atac /yoshitake/test/annotation~BRAKER2/braker/genome.fa 1>/yoshitake/test/annotation~BRAKER2/braker/augustus.hints.gff 2>/yoshitake/test/annotation~BRAKER2/braker/errors/augustus.hints.stderr # Sat Jan 16 14:12:50 2021: Making a gtf file from /yoshitake/test/annotation~BRAKER2/braker/augustus.hints.gff cat /yoshitake/test/annotation~BRAKER2/braker/augustus.hints.gff | perl -ne 'if(m/\tAUGUSTUS\t/) {print $_;}' | perl /root/Augustus/scripts/gtf2gff.pl --printExon --out=/yoshitake/test/annotation~BRAKER2/braker/augustus.hints.tmp.gtf 2>/yoshitake/test/annotation~BRAKER2/braker/errors/gtf2gff.augustus.hints.gtf.stderr # Sat Jan 16 14:12:51 2021: Making a fasta file with protein sequences of /yoshitake/test/annotation~BRAKER2/braker/augustus.hints.gtf /root/anaconda3/bin/python3 /root/Augustus/scripts/getAnnoFastaFromJoingenes.py -g /yoshitake/test/annotation~BRAKER2/braker/genome.fa -f /yoshitake/test/annotation~BRAKER2/braker/augustus.hints.gtf -o /yoshitake/test/annotation~BRAKER2/braker/augustus.hints 1> /yoshitake/test/annotation~BRAKER2/braker/getAnnoFastaFromJoingenes.augustus.hints_tmp.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/getAnnoFastaFromJoingenes.augustus.hints_tmp.stderr # Sat Jan 16 14:12:52 2021: fixing AUGUSTUS genes with in frame stop codons... /root/anaconda3/bin/python3 /root/Augustus/scripts/fix_in_frame_stop_codon_genes.py -g /yoshitake/test/annotation~BRAKER2/braker/genome.fa -t /yoshitake/test/annotation~BRAKER2/braker/augustus.hints.gtf -b /yoshitake/test/annotation~BRAKER2/braker/bad_genes.lst -o augustus.hints_fix_ifs_ -s run1 -m off --UTR off --print_utr off -a /yoshitake/test/annotation~BRAKER2/config/ -C /usr/bin -A /root/Augustus/bin -S /root/Augustus/scripts -H /yoshitake/test/annotation~BRAKER2/braker/hintsfile.gff -e /root/BRAKER/scripts/cfg/rnaseq.cfg > /yoshitake/test/annotation~BRAKER2/braker/fix_in_frame_stop_codon_genes_augustus.hints.log 2> /yoshitake/test/annotation~BRAKER2/braker/errors/fix_in_frame_stop_codon_genes_augustus.hints.err # Sat Jan 16 14:13:03 2021: Moving gene prediction file without in frame stop codons to location of original file (overwriting it)... mv /yoshitake/test/annotation~BRAKER2/braker/augustus.hints_fix_ifs_.gtf /yoshitake/test/annotation~BRAKER2/braker/augustus.hints.gtf # Sat Jan 16 14:13:03 2021: Deleting file with genes with in frame stop codons... rm /yoshitake/test/annotation~BRAKER2/braker/bad_genes.lst # Sat Jan 16 14:13:03 2021: Making a fasta file with protein sequences of /yoshitake/test/annotation~BRAKER2/braker/augustus.hints.gtf /root/anaconda3/bin/python3 /root/Augustus/scripts/getAnnoFastaFromJoingenes.py -g /yoshitake/test/annotation~BRAKER2/braker/genome.fa -f /yoshitake/test/annotation~BRAKER2/braker/augustus.hints.gtf -o /yoshitake/test/annotation~BRAKER2/braker/augustus.hints 1> /yoshitake/test/annotation~BRAKER2/braker/getAnnoFastaFromJoingenes.augustus.hints_hints.stdout 2>/yoshitake/test/annotation~BRAKER2/braker/errors/getAnnoFastaFromJoingenes.augustus.hints_hints.stderr # Sat Jan 16 14:13:04 2021: AUGUSTUS prediction complete # Sat Jan 16 14:13:04 2021: Trying to create merged gene set from GeneMark-EX and AUGUSTUS predictions (braker.gtf/braker.utr.gtf)... perl /root/BRAKER/scripts/merge_transcript_sets.pl /yoshitake/test/annotation~BRAKER2/braker/augustus.hints.gtf /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.f.multi_anchored.gtf 1> /yoshitake/test/annotation~BRAKER2/braker/braker.gtf 2>/yoshitake/test/annotation~BRAKER2/braker/errors/merge_transcripts_multi_anchored.stderr mv /yoshitake/test/annotation~BRAKER2/braker/braker.gtf /yoshitake/test/annotation~BRAKER2/braker/step2.gtf perl /root/BRAKER/scripts/merge_transcript_sets.pl /yoshitake/test/annotation~BRAKER2/braker/step2.gtf /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.f.single_anchored.gtf 1> /yoshitake/test/annotation~BRAKER2/braker/braker.gtf 2>/yoshitake/test/annotation~BRAKER2/braker/errors/merge_transcripts_single_anchored.stderr # Sat Jan 16 14:13:05 2021: deleting empty files # Sat Jan 16 14:13:05 2021: find /yoshitake/test/annotation~BRAKER2/braker -empty rm /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.f.bad.gtf rm /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.f.single_anchored.gtf rm /yoshitake/test/annotation~BRAKER2/braker/errors/find_python3_re.err rm /yoshitake/test/annotation~BRAKER2/braker/errors/find_python3_biopython.err rm /yoshitake/test/annotation~BRAKER2/braker/errors/new_species.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/bam2hints.0.stdout rm /yoshitake/test/annotation~BRAKER2/braker/errors/bam2hints.0.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/join_mult_hints.rnaseq.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/filterIntronsFindStrand.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/filterGenemark.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/downsample_traingenes.err rm /yoshitake/test/annotation~BRAKER2/braker/errors/traingenes.gtf_gff2gbSmallDNA.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/filterGenesIn_mRNAname.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/etrainFilterGenes.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/filterGenesIn.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/randomSplit.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/firstetraining.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/firsttest.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/optimize_augustus.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/secondetraining.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/secondtest.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/augustus.hints.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/gtf2gff.augustus.hints.gtf.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/getAnnoFastaFromJoingenes.augustus.hints_tmp.stderr rm /yoshitake/test/annotation~BRAKER2/braker/errors/fix_in_frame_stop_codon_genes_augustus.hints.err rm /yoshitake/test/annotation~BRAKER2/braker/errors/getAnnoFastaFromJoingenes.augustus.hints_hints.stderr rm /yoshitake/test/annotation~BRAKER2/braker/tmp_no_merge_hints.gff rm /yoshitake/test/annotation~BRAKER2/braker/singlecds.hints rm /yoshitake/test/annotation~BRAKER2/braker/ensure_min_n_training_genes.stdout rm /yoshitake/test/annotation~BRAKER2/braker/downsample_traingenes.log rm /yoshitake/test/annotation~BRAKER2/braker/fix_in_frame_stop_codon_genes_augustus.hints.log rm /yoshitake/test/annotation~BRAKER2/braker/getAnnoFastaFromJoingenes.augustus.hints_hints.stdout # Sat Jan 16 14:13:05 2021: deleting job lst files (if existing) rm /yoshitake/test/annotation~BRAKER2/braker/traingenes.gtf rm /yoshitake/test/annotation~BRAKER2/braker/good_genes.lst rm /yoshitake/test/annotation~BRAKER2/braker/train.f.gb rm /yoshitake/test/annotation~BRAKER2/braker/gbFilterEtraining.stdout rm /yoshitake/test/annotation~BRAKER2/braker/etrain.bad.lst rm /yoshitake/test/annotation~BRAKER2/braker/train.ff.gb rm /yoshitake/test/annotation~BRAKER2/braker/traingenes.good.gtf rm /yoshitake/test/annotation~BRAKER2/braker/traingenes.good.fa rm /yoshitake/test/annotation~BRAKER2/braker/aa2nonred.stdout rm /yoshitake/test/annotation~BRAKER2/braker/traingenes.good.nr.fa rm /yoshitake/test/annotation~BRAKER2/braker/nonred.loci.lst rm /yoshitake/test/annotation~BRAKER2/braker/train.gb.train rm /yoshitake/test/annotation~BRAKER2/braker/train.gb.test rm /yoshitake/test/annotation~BRAKER2/braker/train.gb.train.train rm /yoshitake/test/annotation~BRAKER2/braker/train.gb.train.test rm /yoshitake/test/annotation~BRAKER2/braker/firstetraining.stdout rm /yoshitake/test/annotation~BRAKER2/braker/secondetraining.stdout rm /yoshitake/test/annotation~BRAKER2/braker/augustus.hints.tmp.gtf rm /yoshitake/test/annotation~BRAKER2/braker/fix_IFS_log_ruszdnkw perl /root/BRAKER/scripts/braker_cleanup.pl --wdir=/yoshitake/test/annotation~BRAKER2/braker Deleting file /yoshitake/test/annotation~BRAKER2/braker/firsttest.stdout Deleting file /yoshitake/test/annotation~BRAKER2/braker/genome.fa Deleting file /yoshitake/test/annotation~BRAKER2/braker/optimize_augustus.stdout Deleting file /yoshitake/test/annotation~BRAKER2/braker/secondtest.stdout Deleting file /yoshitake/test/annotation~BRAKER2/braker/train.gb Deleting file /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.d.gtf Deleting file /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.f.good.gtf Deleting file /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.c.gtf Deleting file /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/genemark.average_gene_length.out Deleting file /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/gmes.log Deleting file /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/run.cfg Deleting file /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET.stdout Deleting file /yoshitake/test/annotation~BRAKER2/braker/filterGenemark.stdout Deleting file /yoshitake/test/annotation~BRAKER2/braker/genome.fa.cidx Deleting file /yoshitake/test/annotation~BRAKER2/braker/getAnnoFastaFromJoingenes.augustus.hints_tmp.stdout Deleting file /yoshitake/test/annotation~BRAKER2/braker/augustus.hints.gff Deleting directory /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/data Deleting directory /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/info Deleting directory /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/output Deleting directory /yoshitake/test/annotation~BRAKER2/braker/GeneMark-ET/run #********************************************************************************** # BRAKER RUN FINISHED #**********************************************************************************