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MARVEL: Metagenomic Analyses and Retrieval of Viral ELements
License: GNU General Public License v3.0
This project forked from laboratoriobioinformatica/marvel
MARVEL: Metagenomic Analyses and Retrieval of Viral ELements
License: GNU General Public License v3.0
According to this, with newer versions of scikit-learn
the forest
module has been renamed to sklearn.ensemble._forest
.
So, create a fresh environment with
$ conda create -n marvel hmmer prokka numpy scipy biopython=1.75 scikit-learn=0.21.3
Same goes for biopython
, I was getting some AlignIO related error. Once rolling back to 1.75 it was fixed.
If the input is large enough to be processed, but does not produce a valid fasta file (i.e. empty), hmm fails. It would be nice to keep going and analyze all other bins/contigs that do have some proteins predicted.
Possible fix:
remove all prokka dirs that have an empty fasta file. Then these are input to hmm and everyone is happy.
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