========================================================== Starting on : Fri May 7 13:00:06 EDT 2021 Running on node : scc-pi1 Current directory : /project/scv/examples/bioinformatics/gatk Current job ID : 6400063 Current job name : gatk_SRR062634_200 Number of cores: 2 ========================================================== time fastq-dump -X 200 --split-e SRR062634 Read 200 spots for SRR062634 Written 200 spots for SRR062634 real 0m1.710s user 0m0.055s sys 0m0.018s time bwa mem -a -M -t 2 /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.fasta /project/scv/examples/bioinformatics/gatk/data/SRR062634_X200/SRR062634_1.fastq /project/scv/examples/bioinformatics/gatk/data/SRR062634_X200/SRR062634_2.fastq > /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-bwa.sam 2> /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-bwa.err real 0m48.659s user 0m0.437s sys 0m5.817s 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_200_6400063/SRR062634-bwa.sam -O /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/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_200_6400063/SRR062634-rgsort.out 2> /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-rgsort.err real 0m1.470s user 0m3.069s sys 0m0.488s 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_200_6400063/SRR062634-sort-rg.bam -O /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-sort-rg-dedup.bam -M /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-dedup-metric.txt --ASSUME_SORT_ORDER coordinate --CREATE_INDEX true > /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-dedup.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-dedup.err real 0m9.948s user 0m37.167s sys 0m7.128s 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_200_6400063/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_200_6400063/SRR062634-realign-targets.intervals > /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-realigntarget.out 2> /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-realigntarget.err real 17m39.096s user 18m10.867s sys 0m28.526s 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_200_6400063/SRR062634-realign-targets.intervals -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-sort-rg-dedup.bam -o /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-sort-rg-dedup-realigned.bam --filter_bases_not_stored >/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-realignbam.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-realignbam.err real 0m19.251s user 0m27.019s sys 0m4.256s 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_200_6400063/SRR062634-sort-rg-dedup-realigned.bam >/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-realignbamindex.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-realignbamindex.err real 0m1.359s user 0m2.234s sys 0m0.472s 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_200_6400063/SRR062634-sort-rg-dedup-realigned.bam -O /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-recal-table.txt >/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-recalibrate.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-recalibrate.err real 0m8.983s user 0m16.078s sys 0m1.463s 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_200_6400063/SRR062634-sort-rg-dedup-realigned.bam -bqsr-recal-file /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-recal-table.txt -O /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-GATK.bam > /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-recalbam.out 2> /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-recalbam.err real 0m4.545s user 0m12.147s sys 0m1.176s 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_200_6400063/SRR062634-GATK.bam >/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-GATKbamindex.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-GATKbamindex.err real 0m1.355s user 0m2.248s sys 0m0.447s 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 HaplotypeCaller -R /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.fasta -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-GATK.bam --dbsnp /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.dbsnp138.vcf -O /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-GATK-HC.vcf >/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-GATK-HC.out 2>/project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-GATK-HC.err real 8m18.686s user 9m1.466s sys 0m8.927s DONE!