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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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gff2tbl error #859

Open lalalagartija opened 1 year ago

lalalagartija commented 1 year ago

Hi, I tried : funannotate gff2tbl -g out.gff -f Z_test.fna I just got this error :

Traceback (most recent call last): File "/home/rigou/Work/Annot_test/venv_annot/bin/funannotate", line 8, in sys.exit(main()) File "/home/rigou/Work/Annot_test/venv_annot/lib/python3.9/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/home/rigou/Work/Annot_test/venv_annot/lib/python3.9/site-packages/funannotate/utilities/gff2tbl.py", line 355, in main dicts2tbl(sortedGenes, scaff2genes, scaffLen, 'CFMR', '12345', File "/home/rigou/Work/Annot_test/venv_annot/lib/python3.9/site-packages/funannotate/utilities/gff2tbl.py", line 36, in dicts2tbl for item in obo_parser.OBOReader(os.path.join(os.environ["FUNANNOTATE_DB"], 'go.obo')): File "/usr/lib/python3.9/os.py", line 679, in getitem raise KeyError(key) from None KeyError: 'FUNANNOTATE_DB'`

This is my gff: Z_vitis GeneMark.hmm gene 40 966 87.062668 - 0 ID=gene1;Name=gene1;Notes=Transmembrane domain Z_vitis GeneMark.hmm mRNA 40 966 87.062668 - 0 ID=gene1.t1;Parent=gene1;Name=gene1;product=zeofijzo Z_vitis GeneMark.hmm CDS 40 966 87.062668 - 0 ID=gene1.cds1;Parent=gene1.t1;Name=gene1;product=zeofijzo Z_vitis GeneMark.hmm gene 6160 7290 60.349689 + 0 ID=gene2;Name=gene2 Z_vitis GeneMark.hmm mRNA 6160 7290 60.349689 + 0 ID=gene2.t1;Parent=gene2;Name=gene2;product=oziejf Z_vitis GeneMark.hmm CDS 6160 7290 60.349689 + 0 ID=gene2.cds1;Parent=gene2.t1;Name=gene2;product=oziejf Z_vitis GeneMark.hmm gene 7345 9174 122.990477 + 0 ID=gene3;Name=gene3 Z_vitis GeneMark.hmm mRNA 7345 9174 122.990477 + 0 ID=gene3.t1;Parent=gene3;Name=gene3;product=foizejf Z_vitis GeneMark.hmm CDS 7345 9174 122.990477 + 0 ID=gene3.cds1;Parent=gene3.t1;Name=gene3;product=foizejf

nextgenusfs commented 1 year ago

The ENV variable FUNANNOTATE_DB is not set so it can't find the file used to convert the go ontology annotations.