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matsen / pplacer

Phylogenetic placement and downstream analysis
http://matsen.fredhutch.org/pplacer/
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'guppy classify --classifier nbc': unaligned sequences cause error without --no-pre-mask #300

Closed nhoffman closed 11 years ago

nhoffman commented 11 years ago

for example:

[nhoffman@rhino2] validate % pwd
/shared/silo_researcher/Matsen_F/MatsenGrp/working/nhoffman/validate
[nhoffman@rhino2] validate % PATH=deps/pplacer/bin guppy classify --nbc-rank genus --nbc-as-rdp --random-tie-break -c /shared/silo_researcher/Matsen_F/MatsenGrp/micro_refset/refset/build/targets/vaginal-full-length/vaginal-full-length-0.3.1-raxml.refpkg --sqlite output/nbc_mock/v1-v2/no-flowsim/nbc-genus-rdplike-randomtie/placements.db --classifier nbc --nbc-sequences output/nbc_mock/v1-v2/no-flowsim/inseqs.fasta -j 4
Didn't find any reference sequences in given alignment file. Using supplied reference alignment.
query S000537507_ts is not the same length as the reference alignment (got 275; expected 2830)
matsen commented 11 years ago

@nhoffman Can you remind me what branch this was fixed in?

matsen commented 11 years ago

@nhoffman Ah, it was #290. Let's talk about what's keeping that from getting merged tomorrow.

matsen commented 11 years ago

This issue closed by merging in branch 290.