Call stage has high memory utilization for large numbers of bounds

quinlan-lab / STRling

Detect novel (and reference) STR expansions from short-read data

MIT License

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Call stage has high memory utilization for large numbers of bounds #32

Closed hdashnow closed 4 years ago

hdashnow commented 4 years ago

Example:

   PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND                                 
   NA  NA          20   0  133.6g  84.4g    676 S 139.8 22.4  31:57.63 strling

Occurs when number of bounds is large due to loci detected in that sample, as well as when a large number of loci are provided with -l as occurs in joint genotyping.

Occurs on release v0.0.1.

hdashnow commented 4 years ago

Solution:
Set threads = 0 in: open(ibam_dist, args.bam, fai=args.fasta, threads=0)

fixed in b00512d4e3badc23832318b2587f0831eb5af82d but not yet merged into master