gatk线程数对标记重复速度的影响

 

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。