Error when running kage index
Opened this issue · 4 comments
Hi,
I'm trying to run the indexing step of kage on my data set but I get the following error:
ValueError: zero-size array to reduction operation maximum which has no identity
My input VCF is quite large, but I managed to reproduce the same error with a small test dataset (attached to this message). I'm using the latest version of kage, installed via pip.
The command I used was:
kage index -r test-reference.fa -v test-variants-bi-AF.vcf.gz -o index -k 31
Best,
Jana
Hi!
Thanks for reaching out! There's been a lot of development on KAGE the last days and unfortunately not so good testing.
I was able to reproduce your error, and I think I have now fixed the bug causing it. It should work now if you install the latest version of kage with pip install kage-genotyper==0.2.5.
Sorry for this and thanks a lot for reporting and providing the example data!
Let me know if you run into any other issues or have questions :)
Great, thanks a lot for your quick reply! I'll test the new version and let you know if it solved the issue.
Ok, I did some experiments with the new version, but now I get a different error when running the index command on my data set. I was able to reproduce the error with a small example. I attached it together with the complete log / error Kage produces when running on this VCF.
It seems like this happens when the reference genome does not have the same chromosome order as the VCF. I've pushed a fix for this now (pip install kage-genotyper==0.2.7 should fix it).
Thanks again for trying out and sharing! :)