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ksamuk / pixy

Software for painlessly estimating average nucleotide diversity within and between populations
https://pixy.readthedocs.io/
MIT License
115 stars 14 forks source link

Error in NUMEXPR dependency #18

Closed mscharmann closed 3 years ago

mscharmann commented 3 years ago

Hello, many thanks for going through a lot of work to spare a lot of people the trouble to force conventional tools into making meaningful statistics in the presence of missing data - I certainly have burned a lot of time doing that with cumbersome approaches, like fake VCFs that only contain read deth information, or bedtools etc to cheat PopGenome into not assuming reference alleles for regions without read coverage etc etc....

Unfortunately, I get this error (have pixy through conda) whatever I do, even with only "pixy --help", get:

Error. nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)

See also: https://github.com/cggh/scikit-allel/issues/285

Cheers, Mathias

mscharmann commented 3 years ago

OK so it helps to just paste this into the pixy executable script in the conda path:

import os os.environ["NUMEXPR_MAX_THREADS"]="272"

kkorunes commented 3 years ago

Hi Mathias-- thanks for using pixy and posting here! It sounds like you have this working now? If not, would you mind posting your full pixy command, your OS, and the version of python you're running (since this error appears to be associated with pandas)? I'll also note that the next version of pixy should be released very soon, and it includes a few key performance improvements, which might alleviate the error you're encountering.

mscharmann commented 3 years ago

Hello, yes many thanks, the issue is resolved for my case - but perhaps you can fix this in an upcoming version.