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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
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bamSitesToWig asking for non-integer number of cores #119

Closed rcorces closed 4 years ago

rcorces commented 5 years ago

After a recent update, I'm getting an error with bamSitesToWig where it calls for a non-integer number of cores via the -p argument: bamSitesToWig.py: error: argument -p/--cores: invalid int value: '5.333333333333333'

This comes from this line which introduces a divide by 3 outside of the int() call: https://github.com/databio/pepatac/blob/a0e4347b199c91bbfd7d994b0705da2ca8d51015/pipelines/pepatac.py#L1036

I was looking back through the git history on this and it looks like a collision of two commits around the same time caused this problem? It looks like this commit had fixed the problem on 3/22: https://github.com/databio/pepatac/commit/2d6e6e17d3db657a7406347496550f389d02c36d

but somehow that commit seems to have gotten unintentionally overwritten by this commit on 3/25: https://github.com/databio/pepatac/commit/2a459539907ca09f9f4514bbf44e64110c7853f1

The difference is the placement of the int()

Log attached but I think I've properly diagnosed the problem?

PEPATAC_log.md.txt

nsheff commented 5 years ago

Yep. I think you're exactly right. in the meantime if you use a number of cores that's divisible by 3 it should go away :).

nsheff commented 5 years ago

@jpsmith5 do you want to correct this?

jpsmith5 commented 5 years ago

It was re-corrected already. Trying to finish up testing dev branch before merging into master, then it'll be corrected there again.

jpsmith5 commented 4 years ago

No longer an issue