search

jpuritz / dDocent

a bash pipeline for RAD sequencing
ddocent.com
MIT License
52 stars 41 forks source link

ulimit silent error (bug) #79

Closed pdimens closed 5 months ago

pdimens commented 3 years ago

I recently had variant calling finish, and somewhere in the terminal log was a minor mention of mawk being unable to open mapped.somenumber.bed because of an open file limit. The issue is that despite this error, freebayes still ran and dDocent still finished, and had I not spotted that single mention of mawk failure, I wouldn't have noticed something was wrong. That instance of freebayes ran for ~24hrs and since changing the ulimit, it's been running >48hrs (and still going), so the error had a pretty substantial impact on how many instances of freebayes dDocent was creating.

I think I isolated the mawk part creating the mapped.??.bed files. Is there a way to introduce logic to this so it will error and exit if it fails, rather than continuing to run freebayes anyway?

https://github.com/jpuritz/dDocent/blob/270bc93fba35b70e041a48ccc9d749122b85fec3/dDocent#L497-L504

jpuritz commented 3 years ago

73a01502425cfdc812299d98ffcc5f01dd78f468 Should fix this. Please test and let me know.