mdmcleaner
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KeyError: 'Bacteria'
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!