Source: minimac4 Version: 1.0.2-3 X-Debbugs-CC: debian...@lists.debian.org Severity: serious User: debian...@lists.debian.org Usertags: regression
Dear maintainer(s),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 1.0.2-3
all others from testing from testing
I copied some of the output at the bottom of this report. Similar to bug
#1000413 I think this issue points at ABI breakage. The following in the
changelog looks very suspicious:
* Rebuild minimac4 against new version of libstatgen This is a hint. The test passes in unstable.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=minimac4 https://ci.debian.net/data/autopkgtest/testing/amd64/m/minimac4/16920779/log.gz-------------------------------------------------------------------------------- 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: 2021-11-11 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 Gathering variant information ...ERROR !!! Empty Value for Individual : TA98 at First Marker Most probably a corrupted VCF file. Please check input VCF file !!! *** stack smashing detected ***: terminated
Aborted autopkgtest [07:10:54]: test run-sample-analysis
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