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brentp / vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5
MIT License
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too many open files #14

Closed sigven closed 8 years ago

sigven commented 8 years ago

Hi @brentp ,

Having downloaded the latest binaries, the too many open files problem has returned. For me, vcfanno works with the Linux binary you created for me previously (http://home.chpc.utah.edu/~u6000771/vcfanno_09b), but not with the latest release.

best, Sigve

brentp commented 8 years ago

could you re-run prefixed by IRELATE_VERBOSE=TRUE with this binary: http://home.chpc.utah.edu/~u6000771/vcfanno_0.10f if it still fails, will you let me know the last 40 or so lines to STDERR?

I've tried to recreate this but am unable to do so this time. I guess you could also check the limits of

$ ulimit -Hn
$ sysctl fs.file-max

but even if I set those quite low, I'm not able to see the error.

brentp commented 8 years ago

... I'll try with the release version and see if I can recreate.

brentp commented 8 years ago

@sigven I am able to re-create with version 0.09 release. but not with the binary that I linked above. I'm working on adding a test-case for this but, it's fixed in master.

sigven commented 8 years ago

@brentp thanks. I ran with the 0.10f binary, and it did not fail now. btw, do you have a similar binary for Mac (darwin)?

brentp commented 8 years ago

thanks for checking. I'll make a pre-release shortly and CC this issue.

brentp commented 8 years ago

... and the pre-release will have a mac binary.

brentp commented 8 years ago

I published a pre-release that's solves this and a number of other smaller issues. Please let me know if you have any more problems.