[Debian-med-packaging] Bug#970340: rna-star: autopkgtest regression: --genomeSAindexNbases 8 is too large for the genome size=99940

[Andreas Tille]

Hi Sascha,

you once wrote that test.  Do you have any idea how to fix it?

Steffen, you know that package.  Any idea what to do?

Kind regards

       Andreas.

On Mon, Sep 14, 2020 at 10:15:12PM +0200, Paul Gevers wrote:
> Source: rna-star
> Version: 2.7.5c+dfsg-1
> X-Debbugs-CC: debian-ci at lists.debian.org
> Severity: serious
> User: debian-ci at lists.debian.org
> Usertags: regression
> 
> Dear maintainer(s),
> 
> With a recent upload of rna-star the autopkgtest of rna-star fails in
> testing when that autopkgtest is run with the binary packages of
> rna-star from unstable. It passes when run with only packages from
> testing. In tabular form:
> 
>                        pass            fail
> rna-star               from testing    2.7.5c+dfsg-1
> all others             from testing    from testing
> 
> I copied some of the output at the bottom of this report.
> 
> Currently this regression is blocking the migration to testing [1]. Can
> you please investigate the situation and fix it?
> 
> More information about this bug and the reason for filing it can be found on
> https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
> 
> Paul
> 
> [1] https://qa.debian.org/excuses.php?package=rna-star
> 
> https://ci.debian.net/data/autopkgtest/testing/amd64/r/rna-star/7008363/log.gz
> 
> autopkgtest [20:08:01]: test command1: [-----------------------
> Sep 13 20:08:01 ..... started STAR run
> Sep 13 20:08:01 ... starting to generate Genome files
> Sep 13 20:08:01 ..... processing annotations GTF
> !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome
> size=99940, which may cause seg-fault at the mapping step. Re-run genome
> generation with recommended --genomeSAindexNbases 7
> Sep 13 20:08:01 ... starting to sort Suffix Array. This may take a long
> time...
> Sep 13 20:08:01 ... sorting Suffix Array chunks and saving them to disk...
> Sep 13 20:08:01 ... loading chunks from disk, packing SA...
> Sep 13 20:08:01 ... finished generating suffix array
> Sep 13 20:08:01 ... generating Suffix Array index
> Sep 13 20:08:01 ... completed Suffix Array index
> Sep 13 20:08:01 ... writing Genome to disk ...
> Sep 13 20:08:01 ... writing Suffix Array to disk ...
> Sep 13 20:08:01 ... writing SAindex to disk
> Sep 13 20:08:01 ..... finished successfully
> Sep 13 20:08:01 ..... started STAR run
> Sep 13 20:08:01 ..... loading genome
> Sep 13 20:08:01 ..... started mapping
> Sep 13 20:08:02 ..... finished mapping
> Sep 13 20:08:02 ..... finished successfully
> autopkgtest [20:08:02]: test command1: -----------------------]
> autopkgtest [20:08:02]: test command1:  - - - - - - - - - - results - -
> - - - - - - - -
> command1             FAIL stderr: !!!!! WARNING: --genomeSAindexNbases 8
> is too large for the genome size=99940, which may cause seg-fault at the
> mapping step. Re-run genome generation with recommended
> --genomeSAindexNbases 7
> 




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