__STDOUT LOG__ Job runs on fgcz-h-901 at /scratch/DNABamStats_new_cmdOptions_2024-11-01--10-30-52_NA12878_chr10_temp2298018 __SCRIPT END__ __STDERR LOG__ + REF=/srv/GT/reference/Homo_sapiens/Ensembl/GRCh37.p13/Annotation/Version-2015-03-05/../../Sequence/WholeGenomeFasta/genome.fa + BAM_FILE=/srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_2024-11-01--10-18-44/NA12878_chr10.bam ++ basename /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_2024-11-01--10-18-44/NA12878_chr10.bam + FN=NA12878_chr10.bam + cp -a /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_2024-11-01--10-18-44/NA12878_chr10.bam . + samstat NA12878_chr10.bam [2024-11-01 10:31:04] SAMstat 1.5.1, Copyright (C) 2014 Timo Lassmann [2024-11-01 10:31:04] cmd: samstat NA12878_chr10.bam [2024-11-01 10:31:04] NA12878_chr10.bam -------------------------------------------------- [2024-11-01 10:31:04] Starting to collect data. [2024-11-01 10:31:06] Training a HMM on mapq > 20 reads. [2024-11-01 10:31:23] Done. [2024-11-01 10:31:23] Training a HMM on 0 <= mapq < 20 reads. [2024-11-01 10:31:24] Done. [2024-11-01 10:31:24] Training a HMM on unmapped reads. [2024-11-01 10:31:25] Done. [2024-11-01 10:31:25] + mv NA12878_chr10.bam.samstat.html NA12878_chr10.samstat.html + unset DISPLAY + qualimap bamqc -bam NA12878_chr10.bam -c -nt 8 --java-mem-size=30G -outdir NA12878_chr10 Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1024m; support was removed in 8.0 + /usr/local/ngseq/packages/Dev/jdk/21/bin/java -Xmx30g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar CollectGcBiasMetrics OUTPUT=NA12878_chr10.gc.dat SUMMARY_OUTPUT=NA12878_chr10.gc.sum.dat INPUT=NA12878_chr10.bam CHART_OUTPUT=NA12878_chr10.picard.pdf ASSUME_SORTED=true REFERENCE_SEQUENCE=/srv/GT/reference/Homo_sapiens/Ensembl/GRCh37.p13/Annotation/Version-2015-03-05/../../Sequence/WholeGenomeFasta/genome.fa VALIDATION_STRINGENCY=LENIENT + rsync -r NA12878_chr10.samstat.html /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/DNABamStats_new_cmdOptions_2024-11-01--10-30-52/ + rsync -r NA12878_chr10 /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/DNABamStats_new_cmdOptions_2024-11-01--10-30-52/ + rsync -r NA12878_chr10.picard.pdf /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/DNABamStats_new_cmdOptions_2024-11-01--10-30-52/ + cd /scratch + rm -rf /scratch/DNABamStats_new_cmdOptions_2024-11-01--10-30-52_NA12878_chr10_temp2298018 + echo __SCRIPT END__