This statement illustrates the in(s)anity of trying to assign taxonomic ID from BLAST best-hit though ... you basically cannot do this.https://twitter.com/strnr/status/1044684262237179904 …
Not quite - if you set max_target_seqs to a high number, then you get a large number of hits sorted by score - which is very different from setting max_target_seqs to '1' (where you'll do a less exhaustive to - but faster, as @arambaut points out - search ('good' vs 'top' hit).
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All that said, there are SO many issues unrelated to this when you only consider the top hit, that I totally agree with you - can't be done. (but probably not strictly because of the 'max_target_seqs' flag).
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Yeah I mean the whole concept is flawed notwithstanding this BLAST bug/feature!
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We’ve found we need to keep increasing that value as the DB size grows too - hard to tune without an exhaustive test set. Forces a very conservative approach which lengthens search time/cost.
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Het laden lijkt wat langer te duren.
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