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exclude-seqs vsearch fails to parse with imported fasta #43

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nbokulich opened this issue Mar 6, 2019 · 1 comment
Closed

exclude-seqs vsearch fails to parse with imported fasta #43

nbokulich opened this issue Mar 6, 2019 · 1 comment

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@nbokulich
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Bug Description
Not sure what the issue is yet, but see forum xref for steps to reproduce and error report.

I can reproduce this error locally with the data.

vsearch is probably outputting blank lines or for some other reason the lines are not being parsed correctly:

File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_quality_control/_blast.py”, line 85, in _extract_hits
query_id, subject_id, query_len, start, end = line.split(’\t’)
ValueError: not enough values to unpack (expected 5, got 1)
@nbokulich
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this is due to CRLF line endings and how vsearch handles these, not a bug in q2-quality-control per se: https://forum.qiime2.org/t/exclude-seqs-error-with-imported-fasta-file/8662/8?u=nicholas_bokulich

closing here. will fix in q2-types instead: qiime2/q2-types#205

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