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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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Error in mob_cluster `NamesToTaxIDs` #141

Closed dfornika closed 1 year ago

dfornika commented 1 year ago

I'm working on building a custom mob-suite database and I'm getting this error:

Traceback (most recent call last):
  File "mob_cluster", line 8, in <module>
    sys.exit(main())
  File "python3.8/site-packages/mob_suite/mob_cluster.py", line 536, in main
    taxids = NamesToTaxIDs(organisms, ETE3DBTAXAFILE)
  File "python3.8/site-packages/mob_suite/utils.py", line 127, in NamesToTaxIDs
    initETE3Database(ETE3DBTAXAFILE)
TypeError: initETE3Database() missing 2 required positional arguments: 'ETE3DBTAXAFILE' and 'logging'

I'm running commit 665e062f47e09f37af3a285c2cd30edd5c11be83 because there is a similar error in the most recent release (v3.1.4). It appears that this may have been missed while fixing #132