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simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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TypeError: reduction operation 'argmax' not allowed for this dtype #77

Closed neptuneyt closed 4 years ago

neptuneyt commented 4 years ago

Hi Simroux, I would appreciate the VirSorter you contributed to the viral study. I installed VirSorter via conda and downloaded the database, and version was 2.0.alpha. It returned "TypeError: reduction operation 'argmax' not allowed for this dtype" in the "log/iter-0/step3-classify/classify-merged.log", image when I run a test viral sequence(see test.fa) with above command

virsorter run -i test.fa -j 100 -w virsorter_classification/; } &>virsorter.log&

test.fa

>NC_001798.2 Human herpesvirus 2 strain HG52, complete genome
AGTCCCCGTCTTGCCGCGCGGGGGCGGGCGCGGGAAAAAAGCCGCGCGGGGGCGCCCGCGGGAAGGCAGCCCCGCGGCGC
GCGGGGGGAGGGGCGGCGCCCGCGGGGGAGCGGCCGGCTCCGGGGGAGGGACGGGGAAGGGGGCGCGCGGGGCTGCCCTG
CCGCCCGCCCGCCGCCGCCGCCCGCCTTCGCGCCCCCCCCCAAAAAACACCCCCCCCGGGGGTTGACTCCCCGGGGGAAA
AGAGGCGGGGCGGGAGTCCCCGTCCTGCCGCCGCCCCTTAAGAGGGCCCGCAACACGGCCCGGGCTGCGCACGCCAGCCG
GGACGGGTGAGTTCGCTAGGCAAGCACGGACTGGCGGTTACACGTGCATGCGTGCCGAGTGAACTCTCCCGCCCCGACGC
GCTCCGGCTCCGGGCCTACGCCGAGCCCAGCCGCCCGCCATGTCCCGCCGCCGGGGTCCCCGCCGCCGGGGTCCCCGGCG
CCGGCCGCGCCCCGGCGCTCCAGCCGTGCCGCGCCCCGGCGCTCCAGCCGTGCCGCGCCCCGGCGCGCTCCCAACCGCAG
ACTCCCAAATGGTCCCTGCGTACGACTCGGGAACCGCGGTCGAGAGCGCGCCGGCCGCGTCCTCGCTCCTGCGGCGCTGG
CTGCTGGTGCCCCAGGCGGACGACAGCGACGACGCGGACTACGCCGGCAACGACGACGCAGAGTGGGCGAACAGCCCCCC
GAGCGAGGGCGGGGGGAAGGCGCCGGAGGCCCCGCACGCCGCGCCTGCCGCCGCCTGCCCCCCGCCGCCGCCGCGCAAGG
AGCGCGGGCCGCAGCGCCCCCTTCCGCCCCACCTGGCGCTACGGCTGCGCACCACGACGGAGTACCTGGCGCGCCTGAGC
CTGCGCCGGCGGCGGCCCCCCGCGTCCCCGCCCGCGGACGCGCCGCGCGGGAAGGTACGCCTCCCCTCCGACCCCCTGAC
GCCCCTCCGACCCCCTGACGCCCCTCCGACCCCCTGACGCCCCTCCGACCCCCTGACGCCCCTCCGACCCCCTGACGCCC
CTCCGACCCCCTGACGCCCCTCCGACCCCCGTGTCTCCCCGCCCGCAGGTGTGCTTCTCGCCGCGCGTGCAGGTGCGCCA
...
simroux commented 4 years ago

Hi,

VirSorter 1 (this repo) is not available via conda. You're trying to install VirSorter 2 (https://github.com/jiarong/VirSorter2), which is still in alpha version, and for which bugs like the one you mention here are still being worked out. From what I can see here, this looks like an issue with some pandas version, but please feel free to fill in an issue on the VirSorter 2 repo, so that Jiarong knows about it and can address it.

Best, Simon