error for COI assignments about crest4

[mimouschka]

Hi,
I have subsampled the fasta file I need to assign to the first 1000 and the last 6000 sequences and have rerun crest assignment with and without the --otu_table option.
I did not manage to reproduce the error…which confirms it is a formatting error in the midori253darn database, leading to an error in the assignment of my fasta, somewhere between the first 1000th and last 6000th position…
(crest4)mibr@cno-0004:/scratch/ssd/fastwork/metabridge/methods_comparisons/2_metabridge_methods_analysis$ crest4 -t 32 --fasta swarm/COI_methods_comp_SWARM_parsed_6000last.fasta -d midori253darn -o crest4/COI/test Running crest4 v.4.3.6 /scratch/ssd/fastwork/metabridge/common/conda/crest4/lib/python3.11/site-packages/Bio/SearchIO/_legacy/__init__.py:12: BiopythonDeprecationWarning: The 'Bio.SearchIO._legacy' module for parsing BLAST plain text output is deprecated and will be removed in a future release of Biopython. Consider generating your BLAST output for parsing as XML or tabular format instead. warnings.warn( Classification ran successfully. Results are placed in 'crest4/COI/test/assignments.txt'. crest4/COI/test/assignments.txt

[lanzen]

I have looked at this issue and it is bascially caused by the DARN part that contains Bacterial COI homologs in Midori having too much depth in the taxonomic tree. This is caused by intermediate ranks that should have been removed. Basically, we don't even care about taxonomic assignments of non-eukaryotic sequences and in the next release I will likely cap them to phylum rank or similar. But, for now, some temporary fix has to be done so that when CREST4 tries to look up what taxonomic rank that a too high depth (beyond "strain") corresponds to, it does not produce this index out of range error. Lucas, can you have a look at this please? I don't feel comfortable enough with the new code base to try to fix it..

[xapple]

The new version of crest that was just published https://pypi.org/project/crest4/4.3.7/ should fix this problem. I would be grateful if you could test and report any problems. Thanks a lot.

[mimouschka]

@xapple I confirm that crest is completing successfully now :)
Thanks