Hi Andreas,
Andreas Tille, on 2020-09-14 08:08:04 +0200:
> On Sun, Sep 13, 2020 at 12:58:41PM +0200, Étienne Mollier wrote:
> > > But this seems to be kind of a random failure since unstable as well as
> > > arm64 and ppc64el in testing are currently OK[3].
> >
> > Thanks for the notice, I tried running the test in several
> > architectures as well. After running a few times autopkgtests,
> > I see the intermittent error indeed, at least on amd64, and
> > i386. Other architectures I tested (arm64, riscv64) didn't show
> > this issue so far; I'm virtualizing them, so maybe Qemu
> > interferes.
[... https://bugs.debian.org/970344 ...]
> Hmmmm, this all sounds complicated. I explicitly put Aaron in To since
> he is an expert in the blast code and might have some idea. From my gut
> feeling we seem to have face some issue inside either blast or biopython
> which became visible by chance when running the kaptive test suite.
I opened #970344 against ncbi-blast+ to document the issue. One
thing that should work, should time become of the essence, would
be to run kaptive.py in single threaded mode, using flag "-t 1":
kaptive.py \
-t 1 \
-a exact_match.fasta \
-k /usr/share/${pkg}/reference_database/Klebsiella_k_locus_primary_reference.gbk \
-o output/test
Maybe it would be worth adding a flaky run multi-threaded in
that case as well, and point to #970344 to indicate where
intermittent results come from.
> > I'm also near finishing packaging Biopython 1.78, so that update
> > might add a bit more entropy into these testings.
>
> Thumbs up for working on Biopython 1.78 - lets see what side effect it
> will have on the issue above.
Alas, I'm afraid the Biopython 1.78 update didn't help in that
matter.
Kind Regards,
--
Étienne Mollier <etienne.mollier@mailoo.org>
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Sent from /dev/pts/2, please excuse my verbosity.
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