001、
[b20223040323@admin1 test]$ ls SRR1770413.sorted.bam SRR1770413.sorted.markdup_metrics.txt SRR1770413.sorted.markdup.bam step4.slurm [b20223040323@admin1 test]$ time gatk --java-options "-Xmx100g -XX:ParallelGCThreads=1" MarkDuplicates -I SRR1770413.sorted.bam -O SRR1770413.sorted.markdup.bam -M SRR1770413.sorted.markdup_metrics.txt &> /dev/null real 0m25.384s user 1m6.923s sys 0m11.393s [b20223040323@admin1 test]$ time gatk --java-options "-Xmx100g -XX:ParallelGCThreads=4" MarkDuplicates -I SRR1770413.sorted.bam -O SRR1770413.sorted.markdup.bam -M SRR1770413.sorted.markdup_metrics.txt &> /dev/null real 0m22.414s user 0m59.113s sys 0m10.882s [b20223040323@admin1 test]$ time gatk --java-options "-Xmx100g -XX:ParallelGCThreads=16" MarkDuplicates -I SRR1770413.sorted.bam -O SRR1770413.sorted.markdup.bam -M SRR1770413.sorted.markdup_metrics.txt &> /dev/null real 0m22.208s user 1m12.264s sys 0m11.621s
没有影响， 单线程即可。
标签：txt,gatk,SRR1770413,数对,线程,markdup,sorted,bam From： https://www.cnblogs.com/liujiaxin2018/p/17744412.html