Keiran Raine wrote: > For BAM in/out yes: > > inputthreads=<[1]> : input helper threads (for inputformat=bam > only, default: 1) > outputthreads=<[1]> : output helper threads (for outputformat=bam > only, default: 1)
bamsort fixmates=1 calmdnm=1 calmdnmreference="$reference" blockmb=40960 inputthreads=8 outputthreads=8 level=9 I="$sample".realignedtogether.BQSR.namesorted.bam O="$sample".realignedtogether.BQSR.namesorted.fixmate.calmd.bam The above takes about 3 cores during input and since much later it starts writing output it takes 8 cores. Maybe just because of the extreme output compression only. But definitely, it outperformed "samtools clamd" step doing half of the work (just MD: tag calculations). Actually, processing the whole file took maybe 2 minutes in total? "samtools calmd" ran out of wallclock time limit at 12hrs on a cluster node (running on a single core). Thank you for pointing me to bamsort, I added biobambam2 with libmaus2 to my Gentoo Linux recently (is in science overlay now), so it was simple to call it. Martin ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
