samtools calmd does not really work with name sorted files. It spent all the 12 hours to repeatedly load reference fasta.
Heng On Aug 2, 2016, at 9:47 AM, Martin MOKREJŠ <mmokr...@gmail.com> wrote: > 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 > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
