========================================================== Starting on : Fri May 7 13:00:58 EDT 2021 Running on node : scc-mc2 Current directory : /project/scv/examples/bioinformatics/gatk Current job ID : 6400064 Current job name : gatk_SRR062634_400 Number of cores: 4 ========================================================== time fastq-dump -X 400 --split-e SRR062634 Read 400 spots for SRR062634 Written 400 spots for SRR062634 real 0m2.443s user 0m0.074s sys 0m0.033s time bwa mem -a -M -t 4 /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.fasta /project/scv/examples/bioinformatics/gatk/data/SRR062634_X400/SRR062634_1.fastq /project/scv/examples/bioinformatics/gatk/data/SRR062634_X400/SRR062634_2.fastq > /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-bwa.sam 2> /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-bwa.err real 0m47.288s user 0m0.639s sys 0m4.206s time java -Djava.io.tmpdir=/project/scv/examples/bioinformatics/gatk/tmp/ -jar /share/pkg.7/picard/2.25.2/install/bin/picard.jar AddOrReplaceReadGroups -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-bwa.sam -O /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-sort-rg.bam --SORT_ORDER coordinate --CREATE_INDEX true --RGID SRR062634-LANE001 --RGSM SRR062634 --RGLB SRR062634 --RGPL illumina --RGPU SRR062634 > /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-rgsort.out 2> /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-rgsort.err real 0m1.795s user 0m3.286s sys 0m0.288s time java -Djava.io.tmpdir=/project/scv/examples/bioinformatics/gatk/tmp/ -jar /share/pkg.7/picard/2.25.2/install/bin/picard.jar MarkDuplicates -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-sort-rg.bam -O /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-sort-rg-dedup.bam -M /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-dedup-metric.txt --ASSUME_SORT_ORDER coordinate --CREATE_INDEX true > /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-dedup.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-dedup.err real 0m7.013s user 0m18.116s sys 0m2.920s The following have been reloaded with a version change: 1) gatk/4.2.0.0 => gatk/3.8-1 time java -Djava.io.tmpdir=/project/scv/examples/bioinformatics/gatk/tmp/ -jar /share/pkg.7/gatk/3.8-1/install/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.fasta -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-sort-rg-dedup.bam -known /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.known_indels.vcf.gz -o /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-realign-targets.intervals > /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-realigntarget.out 2> /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-realigntarget.err real 17m42.097s user 17m59.837s sys 0m12.929s time java -Djava.io.tmpdir=/project/scv/examples/bioinformatics/gatk/tmp/ -jar /share/pkg.7/gatk/3.8-1/install/GenomeAnalysisTK.jar -T IndelRealigner -R /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.fasta -known /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.known_indels.vcf.gz -targetIntervals /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-realign-targets.intervals -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-sort-rg-dedup.bam -o /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-sort-rg-dedup-realigned.bam --filter_bases_not_stored >/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-realignbam.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-realignbam.err real 0m19.721s user 0m29.238s sys 0m1.732s The following have been reloaded with a version change: 1) gatk/3.8-1 => gatk/4.2.0.0 time java -Djava.io.tmpdir=/project/scv/examples/bioinformatics/gatk/tmp/ -jar /share/pkg.7/picard/2.25.2/install/bin/picard.jar BuildBamIndex -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-sort-rg-dedup-realigned.bam >/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-realignbamindex.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-realignbamindex.err real 0m1.337s user 0m2.233s sys 0m0.244s time java -Djava.io.tmpdir=/project/scv/examples/bioinformatics/gatk/tmp/ -jar /share/pkg.7/gatk/4.2.0.0/install/bin/gatk-package-4.2.0.0-local.jar BaseRecalibrator -R /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.fasta -known-sites /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.dbsnp138.vcf -known-sites /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.known_indels.vcf.gz -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-sort-rg-dedup-realigned.bam -O /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-recal-table.txt >/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-recalibrate.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-recalibrate.err real 0m13.563s user 0m16.562s sys 0m0.946s time java -Xmx8g -Djava.io.tmpdir=/project/scv/examples/bioinformatics/gatk/tmp/ -jar /share/pkg.7/gatk/4.2.0.0/install/bin/gatk-package-4.2.0.0-local.jar ApplyBQSR -R /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.fasta -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-sort-rg-dedup-realigned.bam -bqsr-recal-file /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-recal-table.txt -O /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-GATK.bam > /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-recalbam.out 2> /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-recalbam.err real 0m4.915s user 0m12.505s sys 0m0.532s time java -Djava.io.tmpdir=/project/scv/examples/bioinformatics/gatk/tmp/ -jar /share/pkg.7/picard/2.25.2/install/bin/picard.jar BuildBamIndex -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-GATK.bam >/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-GATKbamindex.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-GATKbamindex.err real 0m1.280s user 0m2.209s sys 0m0.230s time java -Xmx24g -Djava.io.tmpdir=/project/scv/examples/bioinformatics/gatk/tmp/ -jar /share/pkg.7/gatk/4.2.0.0/install/bin/gatk-package-4.2.0.0-local.jar HaplotypeCaller -R /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.fasta -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-GATK.bam --dbsnp /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.dbsnp138.vcf -O /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-GATK-HC.vcf >/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-GATK-HC.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-GATK-HC.err real 8m42.686s user 9m22.337s sys 0m3.916s DONE!