Error in creating GenBank files
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mtnouchi commented
I haven't looked into it in detail, but let me report a bug.
When I ran SPADE against an NCBI RefSeq genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/010/525/GCF_000010525.1_ASM1052v1/GCF_000010525.1_ASM1052v1_genomic.gbff.gz) without any options, I got the following error:
Traceback (most recent call last):
File "/home/SPADE/SPADE.py", line 1214, in <module>
spade.run(args.num_threads,[args.t, args.Nk, args.Nw, args.Ng, args.Ns, args.Np, args.Nu, args.Nm, args.Nr, args.Nq, args.Pk, args.Pw, args.Pg, args.Ps, args.Pp, args.Pu, args.Pm, args.Pr, args.Pq, args.v, args.delete, args.mafft, args.blastn, args.blastp])
File "/home/SPADE/SPADE.py", line 83, in run
locus.all()
File "/home/SPADE/SPADE.py", line 434, in all
self.make_feature_all()
File "/home/SPADE/SPADE.py", line 360, in make_feature_all
feats = hra.make_feature()
File "/home/SPADE/SPADE.py", line 1079, in make_feature
location = CompoundLocation(locations)
File "/usr/local/lib/python3.8/site-packages/Bio/SeqFeature.py", line 1206, in __init__
raise ValueError(
ValueError: CompoundLocation should have at least 2 parts, not []
The directory for each repeat is output, and there seems to be no problem with the repeat detection workflow, so it seems to be an issue with the creation of the SeqFeature object in the GenBank file output.