Consider performing taxonomy search using vsearch

[colinbrislawn]

Taxonomy assignment is currently one of the longest steps. blastn running on a single node takes about 6 hours to search 23k OTU centroids against the silva 128 database. vsearch takes 1.5 minutes.

This vsearch command is equivalent to the current blastn command, with a few exceptions:

vsearch -usearch_global $input/OTUs.fna \
  -db /pic/projects/mint/hundo/ref/silvamod128.fasta \
  -maxaccepts 25 -threads 24 --maxrejects 100 \
  -strand plus -id .60 \
  -blast6out $output/vsearch-hits.txt

The largest difference is that the vsearch glocal alignment does not report the same information as blast, so some of the output columns contain less information.

program
blast	OTU_9997	KF712870	92.254	284	18	3	8	289	1	282	8.10E-110	399
vsearch	OTU_9997	KF712870	91.8	282	23	0	1	289	1	1518	-1	0

The hits are not identical, and vsearch consistently scores hits about 1.5% lower.

---

The largest difference is that hundo's LCA script cann't parse the vsearch hits.

hundo lca --min-score -1 --top-fraction .95 OTUs.fna vsearch-hits.txt \
/pic/projects/mint/hundo/ref/silvamod128.map \
/pic/projects/mint/hundo/ref/silvamod128.tre \
$output/OTU_tax.fasta $output/OTU_tax_assignments.tsv

[2018-04-13 12:46 INFO] Parsing BLAST hits
Traceback (most recent call last):
  File "/people/bris469/.conda/envs/hundo/bin/hundo", line 11, in <module>
    sys.exit(cli())
  File "/people/bris469/.conda/envs/hundo/lib/python3.6/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/people/bris469/.conda/envs/hundo/lib/python3.6/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/people/bris469/.conda/envs/hundo/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/people/bris469/.conda/envs/hundo/lib/python3.6/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/people/bris469/.conda/envs/hundo/lib/python3.6/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/people/bris469/.conda/envs/hundo/lib/python3.6/site-packages/hundo/hundo.py", line 111, in run_lca
    lca_node = tree.get_common_ancestor(hits.names)
  File "/people/bris469/.conda/envs/hundo/lib/python3.6/site-packages/hundo/crest_classifier.py", line 163, in get_common_ancestor
    lca_path = paths[0]
IndexError: list index out of range

[brwnj]

This is now supported using hundo annotate --aligner vsearch .... Commit of merge is 3db5bba.