Bug#962717: q2-quality-control seems so uncover segfaults in bowtie2
Hi,
since q2-taxa is in new I intended to upload q2-quality-control as well.
I upgraded to latest upstream and added some missing (Build-)Depends.
Unfortunately the autopkgtest contains some "Segmentation fault" errors
which is pretty suspicious. Here is an example:
----------------------------- Captured stdout call -----------------------------
Running external command line application. This may print messages to stdout and/or stderr.
The commands to be run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: bowtie2 -p 1 --sensitive-local --rfg 5,3 -x /tmp/qiime2-archive-nz_ah2oz/32eb5e3e-f571-424d-bd94-2e56e0347c98/data/db -1 /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-7z04bhj3/sample_a_S01_L001_R1_001.fastq.gz -2 /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-7z04bhj3/sample_a_S01_L001_R2_001.fastq.gz -S /tmp/tmpz8r9_mc5
----------------------------- Captured stderr call -----------------------------
Segmentation fault
(ERR): Description of arguments failed!
Exiting now ...
I wonder whether someone could try to reproduce this actual call that
might possibly fail not only in the context of q2-quality-control but
in general with bowtie2.
Kind regards
Andreas.
--
http://fam-tille.de
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