Pi calculation error - ValueError: Cannot convert non-finite values (NA or inf) to integer about pixy HOT 4 CLOSED

Hmm, that's a tough one. The repaired version is now up on conda-forge, would it be possible to try a re-install via conda in your snakemake environment? Alternatively, could you try to see if you get this error outside of your custom environment (e.g. in a fresh pixy environment)? Also, maybe a quick fix: if this is a df size limit thing in pandas, try reducing the chunk size to something like '--chunk_size 50000'. Let me know how it goes!

from pixy.

Thanks so much for the quick reply! And apologies, forgot to share my original command but I did try '--chunk_size 50000' for the previous run. Currently running in a fresh pixy environment and will share the outcome :)

from pixy.

Sounds good! You can actually go even lower on the chunk size, (e.g. 10000, the same as the window size), although there is performance decrease.

from pixy.

Success with the fresh environment! Seems like it's an issue with the snakemake env. Thanks!

from pixy.