search

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

attribute error #77

Closed glaudelrio closed 1 year ago

glaudelrio commented 1 year ago

Hi! I am having trouble running pixy... I had worked with it before, and this is the first time this error message is produced...

pixy --stats pi fst dxy --vcf vcf_filtered_075.vcf.gz --populations populations.txt --window_size 50000 --n_cores 8

[pixy] pixy 1.2.4.beta1 [pixy] See documentation at https://pixy.readthedocs.io/en/latest/ AttributeError: module 'allel' has no attribute 'read_vcf_headers'

any idea, on what the issue is? thank you for any help you can provide.

ksamuk commented 1 year ago

Hi There, looks like a combination of an old version of the software (the latest is 1.2.7) and possibly a conflict in your environment. I'd start by installing pixy in a fresh conda environment and trying the same thing again.

glaudelrio commented 1 year ago

Nice! Thank you. Is pixy compatible with python 3.9?

ksamuk commented 1 year ago

I don't think so, at present, but I haven't had time to do extensive testing. We're working on a new major version of pixy, and we'll likely ensure full 3.9 compatibility for that release.

glaudelrio commented 1 year ago

No problem, I got it running on python 3.8. I guess you can close the issue! Thank you for your help. cheers