StrBAMDir + "/pbmm2/v37/"īTW, I use 16 cores to run calmd, however, it looks like the samtools is still using 1 core to run it: top - 11:44:53 up 47 days, 20:35, 1 user, load average: 2.00, 2.01, 2.00 Here is the code I used to add MD tag (very normal): rule addMDTag: In this way, 50GB BAM will take 30days to be finished! The amount of memory used by samtools sort -m is per thread, so if we have 4 threads and 8 Gb of memory given to SLURM (sik.config: samtoolsSortMem. Dec Download the tools Samtools echo 'Start to download Samtools. (4 processors per node with 8 cores each, and I guess 4 threads spawning on each core.) My sysadmin speculates that this is inefficient with regard to memory. The issue that I encountered is that the speed of "calmd" is incredibly slow! The jobs have already run 12 hours, and only 600MB BAM with MD tag are generated. more than one processor being used by multiple threads of your process. The size of original BAM is around 50Gb (whole genome sequence by using pacbio HIFI reads). I am using "samtools calmd" to add MD tag back to BAM file.
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