Good day, Étienne Mollier, on 2020-09-15 00:05:35 +0200: > 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 tried running a few times the kaptive test a few times in a row without "-t 1" and I haven't reproduced the problem after upgrade of ncbi-blast+ to version 2.10.1-1. Thanks Aaron for having kept track of the tblastn issue with multi-threading! Kind Regards, -- Étienne Mollier <etienne.moll...@mailoo.org> Old rsa/3072: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d New rsa/4096: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity.
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