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