`samtools sort` is often creating millions of temp files, and google'ing
hasn't led me to any other posts about this. Mostly people are reporting a
problem with ~1000 files, which is resolved by using ulimit. That's not our
issue. Our BAM files are only 1 - 3 Gb, and we have run on nodes with 8 or
16 Gb of RAM. We've set the -m parameter, but we still get messages like
this to stderr:
[bam_sort_core] merging from 83155297 files...
open: Too many open files
We're using samtools version 0.1.19. Has anyone seen this before?
We were told by our collaborators to use version 0.1.19, but anyone have
thoughts on using a more recent version. Are there significant differences
between 0.1.19 and 1.2?
Just to make sure, is it correct that the -m parameter takes the memory per
thread? Or should we provide the total RAM available for all threads? The
documentation says the former, but I want to double check since the latter
was implied by some possibly unreliable source on the internet. (The above
error is not affected. We've tried both.)
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