[Debian-med-packaging] Bug#964101: Help from bioinformaticians needed! (Was: Bug#964101: tiddit: generates extremely large file during autopkgtesting)

[Andreas Tille]

Control: tags -1 help

See below.  Please help Nilesh finding a smaller data set.

Thank you

    Andreas.

On Thu, Jul 02, 2020 at 05:50:35PM +0530, Nilesh Patra wrote:
> Hi,
> 
> I'm afraid that might not be possible :/
> Tried looking for a smaller data, but as you'd know, the size of 'bam'
> files is huge
> And the output of tiddit seems to result in a huge file too.
> I'll meanwhile try to get a sensible dataset, but I doubt if it's feasible.
> Maybe we'll need to remove the tests in this case.
> 
> Regards,
> Nilesh
> 
> On Thu, 2 Jul 2020, 01:23 Andreas Tille, <tille at debian.org> wrote:
> 
> > Hi Nilesh,
> >
> > may be we can use some smaller data set?
> >
> > Kind regards
> >
> >      Andreas.
> >
> > ----- Forwarded message from Paul Gevers <elbrus at debian.org> -----
> >
> > Date: Wed, 1 Jul 2020 21:07:39 +0200
> > From: Paul Gevers <elbrus at debian.org>
> > To: submit at bugs.debian.org
> > Subject: Bug#964101: tiddit: generates extremely large file during
> > autopkgtesting
> > X-Debian-PR-Message: report 964101
> > X-Debian-PR-Package: src:tiddit
> > X-Debian-PR-Keywords:
> > X-Debian-PR-Source: tiddit
> >
> > Source: tiddit
> > Version: 2.12.0+dfsg-2
> > Severity: serious
> > X-Debbugs-CC: debian-ci at lists.debian.org
> > User: debian-ci at lists.debian.org
> > Usertags: -1 issue
> >
> > Dear maintainer(s),
> >
> > In the last upload of the tiddit package, an autopkgtest was added,
> > great. However, the package seems to generate files, and one file is
> > growing to at least 29 GB. Maybe bigger, but with that size, the VM as
> > runs on several of our arm64 workers is full (total size is 40 GB).
> >
> > root at ci-182-f37c0a21
> > :/tmp/autopkgtest-lxc.mk9f7rok/downtmp/autopkgtest_tmp#
> > ls -alh
> > total 29G
> > drwxr-xr-x 2 debci debci 4.0K Jun 30 22:29 .
> > drwxrwxrwx 5 root  root  4.0K Jun 30 22:29 ..
> > -rw-r--r-- 1 debci debci 1.4M Jun 30 22:19 normal.bam
> > -rw-r--r-- 1 debci debci 5.8M Jun 28 10:11 normal.sam
> > -rw-r--r-- 1 debci debci  11M Jun 28 10:10 ref.fa
> > -rw-r--r-- 1 debci debci    0 Jun 30 22:29 test1.db
> > -rw-r--r-- 1 debci debci    0 Jun 30 22:29 test1.gc.wig
> > -rw-r--r-- 1 debci debci  29G Jun 30 22:22 test1.sample.bam
> > -rw-r--r-- 1 debci debci    0 Jun 30 22:29 test1.signals.tab
> > -rw-r--r-- 1 debci debci    0 Jun 30 22:29 test1.wig
> > -rw-r--r-- 1 debci debci 1.1M Jun 30 22:19 tumor.bam
> > -rw-r--r-- 1 debci debci 4.5M Jun 28 10:12 tumor.sam
> >
> > Please be a bit more gentle with your tests for our infrastructure. I'll
> > have the ci infrastructure ignore tests on arm64 for now until you close
> > this bug.
> >
> > Paul
> >
> >
> >
> >
> >
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at alioth-lists.debian.net
> >
> > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
> >
> >
> > ----- End forwarded message -----
> >
> > --
> > http://fam-tille.de
> >

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