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KeyError: 'Bacteria'

Open chassenr opened this issue 1 year ago • 4 comments

Hi,

I have been running MDMcleaner on 2 different bin sets. In one run, not all bins were processed without error (see #37). Using the same reference data, I am now getting the following error for the last bin to be processed:

--> writing to output files
        writing detailed contig infos to ./T4-48_bin.49.orig/fullcontiginfos_beforecleanup.tsv
        appending overview data to overview_all_before_cleanup.tsv
        creating output fastas
        creating krona input-table
reference-database contaminations detected during this run: 69
blasting 13 entries with blastx against reference proteins (another 5 entries were too long to blastx efficiently
Traceback (most recent call last):
  File "/bio/Software/anaconda3/envs/mdmcleaner-0.8.3/bin/mdmcleaner", line 10, in <module>
    sys.exit(main())
  File "/bio/Software/anaconda3/envs/mdmcleaner-0.8.3/lib/python3.10/site-packages/mdmcleaner/mdmcleaner.py", line 217, in main
    blacklist_additions = clean.main(args, configs)
  File "/bio/Software/anaconda3/envs/mdmcleaner-0.8.3/lib/python3.10/site-packages/mdmcleaner/clean.py", line 230, in main
    if "contamination" in db_suspects.collective_diamondblast():
  File "/bio/Software/anaconda3/envs/mdmcleaner-0.8.3/lib/python3.10/site-packages/mdmcleaner/review_refdbcontams.py", line 319, in collective_diamondblast
    eval_list.append(self.evaluateornot(self.blastxjobs[x], blastxdone = True))
  File "/bio/Software/anaconda3/envs/mdmcleaner-0.8.3/lib/python3.10/site-packages/mdmcleaner/review_refdbcontams.py", line 283, in evaluateornot
    return_category, return_note = comp.count_contradictions() #todo: redundant. streamline blastcontigs() and countcontradictions() more
  File "/bio/Software/anaconda3/envs/mdmcleaner-0.8.3/lib/python3.10/site-packages/mdmcleaner/review_refdbcontams.py", line 123, in count_contradictions
    domain_counts_expected = domain_counts[comparison_domain] #todo: only in try_except statement for debugging
KeyError: 'Bacteria'

Any advice would be appreciated. Thanks!

chassenr avatar Sep 07 '22 10:09 chassenr