Control: reassign -1 vsearch Control: retitle -1 vsearch: breaks q2-quality-control test suite on ppc64el Control: affects -1 + q2-quality-control
Greetings,
The issue below:
> > self.assertEqual(sorted(obs.index), sorted(
> _dnafastaformats_to_series(self.query_seqs_short).index))
> E AssertionError: Lists differ: ['1111783', '1111867', '1111886']
> != ['1111750', '1111768', '1111783', '1111867', '1111886']
> E
> E First differing element 0:
> E '1111783'
> E '1111750'
> E
> E Second list contains 2 additional elements.
> E First extra element 3:
> E '1111867'
> E
> E - ['1111783', '1111867', '1111886']
> E + ['1111750', '1111768', '1111783', '1111867', '1111886']
> E ? ++++++++++++++++++++++
>
looks to be actually caused by vsearch:
> Command: vsearch --usearch_global
> /tmp/autopkgtest-lxc.p_pskvmx/downtmp/autopkgtest_tmp/q2_quality_control/tests/data/query-sequences-short.fasta
> --id 0.97 --strand both --maxaccepts 1 --maxrejects 0 --db
> /tmp/autopkgtest-lxc.p_pskvmx/downtmp/autopkgtest_tmp/q2_quality_control/tests/data/bacterial-ref-sequences.fasta
> --threads 1 --userfields query+target+ql+qlo+qhi --userout /tmp/tmpbvtklulf
>
> ----------------------------- Captured stderr call
> -----------------------------
[…]
> Matching unique query sequences: 3 of 5 (60.00%)
Extracting q2-quality-control test data, to run them against
standalone vsearch raises discrepancies in vsearch results:
- on amd64:
$ vsearch \
--usearch_global query-sequences-short.fasta
--id 0.97 --strand both --maxaccepts 1 \
--maxrejects 0 \
--db bacterial-ref-sequences.fasta --threads 1 \
--userfields query+target+ql+qlo+qhi \
--userout output.amd64
[…]
Matching unique query sequences: 5 of 5 (100.00%)
$ cat output.amd64
1111886 1111886 15 1 15
1111867 1111867 15 1 15
1111783 1111783 15 1 15
1111768 1111768 15 1 15
1111750 1111750 15 1 15
- on ppc64el:
$ vsearch \
--usearch_global query-sequences-short.fasta
--id 0.97 --strand both --maxaccepts 1 \
--maxrejects 0 \
--db bacterial-ref-sequences.fasta --threads 1 \
--userfields query+target+ql+qlo+qhi \
--userout output.ppc64el
[…]
Matching unique query sequences: 3 of 5 (60.00%)
$ cat output.ppc64el
1111886 1111886 15 1 15
1111867 1111867 15 1 15
1111783 1111783 15 1 15
I reassign the bug accordingly.
Kind Regards,
--
Étienne Mollier <emoll...@emlwks999.eu>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/4, please excuse my verbosity.
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