[Debian-med-packaging] Bug#943897: minimac4: autopkgtest regression: Program could NOT open file : targetStudy.vcf.gz

[Paul Gevers]

Source: minimac4
Version: 1.0.2-1
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: regression

Dear maintainers,

With a recent upload of minimac4 the autopkgtest of minimac4 fails in
testing when that autopkgtest is run with the binary packages of
minimac4 from unstable. It passes when run with only packages from
testing. In tabular form:
                       pass            fail
minimac4               from testing    1.0.2-1
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? If needed, please
change the bug's severity.

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=minimac4

https://ci.debian.net/data/autopkgtest/testing/amd64/m/minimac4/3300655/log.gz

autopkgtest [04:55:11]: test run-sample-analysis: [-----------------------


 --------------------------------------------------------------------------------
          Minimac4 - Fast Imputation Based on State Space Reduction HMM
 --------------------------------------------------------------------------------
           (c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds
                             Mary Kate Wing, Goncalo Abecasis

 Version: 1.0.2;
 Built: 2019-10-14 by Reproducible

 Command Line Options:
       Reference Haplotypes : --refHaps [refPanel.m3vcf.gz], --passOnly,
                              --rsid, --referenceEstimates [ON],
                              --mapFile [docs/geneticMapFile.b38.map.txt.gz]
          Target Haplotypes : --haps [targetStudy.vcf.gz]
          Output Parameters : --prefix [testRun], --estimate, --nobgzip,
                              --vcfBuffer [200], --format [GT,DS],
                              --allTypedSites, --meta, --memUsage
        Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb
[3.00]
          Subset Parameters : --chr [], --start, --end, --window
   Approximation Parameters : --minimac3, --probThreshold [0.01],
                              --diffThreshold [0.01], --topThreshold [0.01]
           Other Parameters : --log, --help, --cpus [5], --params
                  PhoneHome : --noPhoneHome [ON], --phoneHomeThinning [50]


 URL = http://genome.sph.umich.edu/wiki/Minimac4
 Starting Main Imputation/Estimation Analysis ...

 Performing preliminary check on input parameters...

 ------------------------------------------------------------------------------
                             PRELIMINARY FILE CHECK

 ------------------------------------------------------------------------------

 Checking GWAS haplotype file : targetStudy.vcf.gz

 ERROR !!!
 Program could NOT open file : targetStudy.vcf.gz

 Program Exiting ...

autopkgtest [04:55:12]: test run-sample-analysis: -----------------------]

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