Error when extracting a certain lineage

[hoelzer]

Maybe it's because my installation of covsonar is not uptodate. If so, and this is not reproducible in the current code, please just close it.

python3 sonar.py match --db gisaid.db --tsv --lineage BQ.1

Error:

Traceback (most recent call last):
  File "/scratch/hoelzerm/git/covsonar/sonar.py", line 529, in <module>
    snr.match_genomes(include_profiles=args.include, exclude_profiles=args.exclude, accessions=args.acc, lineages=args.lineage, with_sublineage=args.with_sublineage, zips=args.zip, dates=args.date, submission_dates=args.submission_date, labs=args.lab, sources=args.source, collections=args.collection, technologies=args.technology, platforms=args.platform, chemistries=args.chemistry, software=args.software, software_version=args.version, materials=args.material, min_ct=args.min_ct, max_ct=args.max_ct, ambig=args.ambig, count=args.count, frameshifts=frameshifts, tsv=args.tsv)
  File "/scratch/hoelzerm/git/covsonar/sonar.py", line 300, in match_genomes
    rows = self.db.match(include_profiles=include_profiles, exclude_profiles=exclude_profiles, accessions=accessions, lineages=lineages, with_sublineage=with_sublineage, zips=zips, dates=dates, submission_dates=submission_dates, labs=labs, sources=sources, collections=collections, technologies=technologies, chemistries=chemistries, software=software, software_version=software_version, materials=materials, min_ct=min_ct, max_ct=max_ct, ambig=ambig, count=count, frameshifts=frameshifts, debug=debug)
  File "/scratch/hoelzerm/git/covsonar/lib/sonardb.py", line 3012, in match
    rows[i]['dna_profile'] = self.filter_ambig(rows[i]['dna_profile'], self.iupac_explicit_nt_code, keep)
  File "/scratch/hoelzerm/git/covsonar/lib/sonardb.py", line 2623, in filter_ambig
    for mutation in list(filter(None, profile.split(" "))):
AttributeError: 'NoneType' object has no attribute 'split'

[hoelzer]

--lineage BQ% --with-sublineage

gives me the same error

[hoelzer]

python sonar.py --version sonar.py 1.1.4

[hoelzer]

same problem with sonar.py 1.1.8

[hoelzer]

THe command works with the rki.db though

[hoelzer]

It works for Sofia in v1.1.7 though... weird...

[stephan-fuchs]

I am marking this issue as closed, as it appears to be an individual system problem. However, please do let me know if the issue persists or if you require any further assistance. Thank you for bringing this to our attention and for your cooperation in resolving the matter.