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INFO:iss.app:Starting iss generate
INFO:iss.app:Using kde ErrorModel
INFO:iss.download:Searching for bacteria to download
Traceback (most recent call last):
File "/lustre2/scratch/shahab/conda/iss/bin/iss", line 10, in <module>
sys.exit(main())
File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/iss/app.py", line 608, in main
args.func(args)
File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/iss/app.py", line 99, in generate_reads
g, n, args.output + '_ncbi_genomes.fasta')
File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/iss/download.py", line 51, in ncbi
id=ident))["DocumentSummarySet"]["DocumentSummary"][0]
File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/Bio/Entrez/__init__.py", line 508, in read
record = handler.read(handle)
File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/Bio/Entrez/Parser.py", line 304, in read
self.parser.ParseFile(handle)
File "/home/conda/feedstock_root/build_artifacts/python_1613748395163/work/Modules/pyexpat.c", line 417, in StartElement
File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/Bio/Entrez/Parser.py", line 581, in startElementHandler
raise ValidationError(tag)
Bio.Entrez.Parser.ValidationError: Failed to find tag 'AssemblyStatusSort' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False.
can probably be fixed adding validate=False to the Entrez.read calls
The text was updated successfully, but these errors were encountered:
Happens on some machines:
can probably be fixed adding
validate=False
to theEntrez.read
callsThe text was updated successfully, but these errors were encountered: