Hi Andreas, Andreas Tille, on 2020-09-13 08:39:20 +0200: > the new version (0.7.3) of kaptive[1] fails its autopkgtest: > > + kaptive.py -a exact_match.fasta -k > /usr/share/kaptive/reference_database/Klebsiella_k_locus_primary_reference.gbk > -o output/test > /usr/lib/python3/dist-packages/Bio/GenBank/__init__.py:1287: > BiopythonParserWarning: The NCBI states double-quote characters like " should > be escaped as "" (two double - quotes), but here it was not: > 'undecaprenyl-phosphate galactose phosphotransferase" glucose-1-phosphate > transferase' > warnings.warn( > Error: tblastn crashed! > > > Interestingly also the old version shows currently an issue in > testing on amd64[2]: > > + kaptive.py -a exact_match.fasta -k > /usr/share/kaptive/reference_database/Klebsiella_k_locus_primary_reference.gbk > -o output/test > Error: tblastn crashed! > > > 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.
My kernel traps a general protection fault in libblast.so during
tblastn execution:
$ sudo dmesg
[...]
[1741071.802876] traps: tblastn[3579372] general protection fault
ip:7ff551327dde sp:7ffdb8072790 error:0 in libblast.so[7ff55130f000+63000]
Looking up into straces, it seems the condition occurs when the
program frees its memory before handing back the hand to the
system, so maybe something in the taste of a double free while
threads are not well aligned. I'm not sure yet of the exact
reproducer with the tblastn command, here is what I record in my
`ps` output; some of the files referenced are temporary
artifacts obtained from former steps of the script:
/usr/bin/tblastn -db_gencode 11 -seg no -db
/tmp/autopkgtest.DOVsFP/autopkgtest_tmp/exact_match.fasta -query
/tmp/autopkgtest.DOVsFP/autopkgtest_tmp/output/kaptive_temp_3600033_520819/temp_gene_seqs.fasta
-num_threads 4 -outfmt 6 qseqid sseqid qstart qend sstart send evalue bitscore
length pident qlen qseq sseq
I'm also near finishing packaging Biopython 1.78, so that update
might add a bit more entropy into these testings.
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/5, please excuse my verbosity.
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