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kage-genotyper / kage

Alignment-free genotyper for SNPs and short indels, implemented in Python.
GNU General Public License v3.0
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Error when running kage index #6

Open eblerjana opened 7 months ago

eblerjana commented 7 months ago

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

kage-issue.tar.gz

ivargr commented 7 months ago

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 :)

eblerjana commented 7 months ago

Great, thanks a lot for your quick reply! I'll test the new version and let you know if it solved the issue.

eblerjana commented 6 months ago

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.

kage-issue.tar.gz

ivargr commented 6 months ago

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! :)