Source: libstatgen, minimac4 Control: found -1 libstatgen/1.0.15-1 Control: found -1 minimac4/1.0.2-2 Severity: serious Tags: sid bookworm X-Debbugs-CC: debian...@lists.debian.org User: debian...@lists.debian.org Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of libstatgen the autopkgtest of minimac4 fails in
testing when that autopkgtest is run with the binary packages of
libstatgen from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
libstatgen from testing 1.0.15-1
minimac4 from testing 1.0.2-2
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 of libstatgen to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
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=libstatgen
https://ci.debian.net/data/autopkgtest/testing/amd64/m/minimac4/15927915/log.gz
autopkgtest [21:29:13]: 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: 2019-11-05 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 ...
Segmentation fault
OpenPGP_signature
Description: OpenPGP digital signature
