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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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RuntimeWarning #124

Closed vappiah closed 2 years ago

vappiah commented 3 years ago

Hi, when running staramr with the settings staramr search --pointfinder-organism salmonella -o starout dir/*.fasta I got the error below. Please advice and thanks apps/Python/Python-3.5/lib/python3.5/site-packages/numpy/core/_methods.py:26: RuntimeWarning: invalid value encountered in reduce return umr_maximum(a, axis, None, out, keepdims)

apetkau commented 3 years ago

Hello @jotes35. Do you happen to have the input files you were using when that warning occurred? Or, was there other messages around that warning message?

Based on some searches, it seems like this warning is generated due to empty/NA values turning up when trying to find the maximum of a list of numbers, which are unexpected (https://github.com/numpy/numpy/issues/11029). Without having more details, though, it's difficult to know what is triggering this.

I do not suspect it will impact your results though, as it is only a warning, but I would need more details to be certain.