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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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running antiSMASH error #819

Open Rahimlou opened 2 years ago

Rahimlou commented 2 years ago

I get the following error by running antiSMASH using "funannotate remote" command.

from Bio.Align import _aligners ImportError: cannot import name '_aligners' from 'Bio.Align'

my code: module load py-antismash/6-1-1 funannotate remote -i Gene_Prediction -m antismash -e email@server.edu -o xxx

hyphaltip commented 2 years ago

can you check what version of biopython you have installed?

nextgenusfs commented 2 years ago

Not sure what your system setup is, but funannotate remote would send the data to the antiSMASH service -- I think this might be broken with update to version 6. But if you are loading a module here and trying to run locally -- that is not what funannotate remote does -- it was originally setup as a convenience when installing antismash locally was not possible. Recommended way would now be to run antismash locally via ronda-mediated install (separate environment) and then you an pass those data to funannotate annotate via the --antismash cmd line option.

Rahimlou commented 2 years ago

Not sure what your system setup is, but funannotate remote would send the data to the antiSMASH service -- I think this might be broken with update to version 6. But if you are loading a module here and trying to run locally -- that is not what funannotate remote does -- it was originally setup as a convenience when installing antismash locally was not possible. Recommended way would now be to run antismash locally via ronda-mediated install (separate environment) and then you an pass those data to funannotate annotate via the --antismash cmd line option.

Exactly, this is the best idea to run antismash individually. I could install the antismash and downloaded the relevant databases. May I know which files from the gene prediction step I should use as the input to antismash? I used .gbk and .gff3, but I got the following error: ValueError: Need a Nucleotide or Protein alphabet

nextgenusfs commented 2 years ago

You would pass the GBK file from predict or update (if you had RNA seq).

Rahimlou commented 2 years ago

Yes, I have RNA seq. How can I update it? Is there a manual to do it?