[Debian-med-packaging] Bug#1021995: fastqtl: autopkgtest regression

[Adrian Bunk]

Source: fastqtl
Version: 2.184+v7+dfsg-2
Severity: serious

https://ci.debian.net/data/autopkgtest/testing/amd64/f/fastqtl/27230464/log.gz

...
autopkgtest [23:13:45]: test run-sample-analysis: [-----------------------
covariates.txt.gz
genotypes.vcf.gz
genotypes.vcf.gz.tbi
interaction.txt
phenotypes.bed.gz
phenotypes.bed.gz.tbi

Fast QTL
  * Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS
  * Contact : olivier.delaneau at gmail.com
  * Webpage : http://fastqtl.sourceforge.net/
  * Version : v2.184_gtex

Perform permutation based interaction analysis (used to calculate corrected p-values for MPs)
  * Perform 100 permutations
  * Test interaction with term from [interaction.txt]
  * Random number generator is seeded with 1
  * Considering variants within 1e+06 bp of the MPs
  * Using minor allele frequency threshold = 0.0000
  * Using minor allele sample threshold = 0
  * Using INFO field AF threshold = 0.0000
  * Chunk processed 1 / 100

Scanning phenotype data in [phenotypes.bed.gz]
  * 364 phenotypes

Reading phenotype data in [phenotypes.bed.gz]
  * region = 22:17517460-17646177
  * 373 samples included
  * 4 phenotypes included

Reading genotype data in [genotypes.vcf.gz] in VCF format
  * region = 22:16517460-18646177
  * 373 samples included
  * 8580 sites included

Reading covariates in [covariates.txt.gz]
  * 373 samples included
  * 4 covariate(s) included

Reading interaction term in [interaction.txt]
  * 373 samples included

Imputing missing genotypes

Imputing missing phenotypes

Initialize covariate 

Processing gene [ENSG00000237438.1]
  * Number of variants in cis = 7966
  * Beta distribution parameters = 1.0382 2287.7101
  * Progress = 25.0%

Processing gene [ENSG00000177663.8]
  * Number of variants in cis = 8165
  * Beta distribution parameters = 0.7994 2826.0721
  * Progress = 50.0%

Processing gene [ENSG00000183307.3]
  * Number of variants in cis = 8279
  * Beta distribution parameters = 0.9595 9906.5566
  * Progress = 75.0%

Processing gene [ENSG00000069998.8]
  * Number of variants in cis = 8466
  * Beta distribution parameters = 0.9606 4564.2130
  * Progress = 100.0%

Running time: 37 seconds
5d4
< ENSG00000093072.10 8531 1.06453 1772.43 334.203 snp_22_17738177 -948 0.000356058 0.683168 0.649116
autopkgtest [23:14:22]: test run-sample-analysis: -----------------------]
autopkgtest [23:14:22]: test run-sample-analysis:  - - - - - - - - - - results - - - - - - - - - -
run-sample-analysis  FAIL non-zero exit status 1



Likely the files under debian/tests/output_tests/ must be regenerated.