bolt-lmm (2.3.6+dfsg-2) [PTS] [DDPO]

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Git: https://salsa.debian.org/med-team/bolt-lmm.git
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Branch: master
Path: debian/changelog
Browser: https://salsa.debian.org/med-team/bolt-lmm
Last scan: 2022-08-06 03:48:09+00
Next scan: 2022-08-14 11:54:00+00
CI pipeline status: success

Debian changelog in Git:

bolt-lmm (2.3.6+dfsg-2) unstable; urgency=medium

  * Team upload.
  * Packaging update
  * Standards-Version: 4.6.1 (routine-update)

 -- Andreas Tille <tille@debian.org>  Thu, 28 Jul 2022 16:48:04 +0200

This branch is 1 commit ahead of tag debian/2.3.6+dfsg-2

Git log:

commit 50badf3338741e739b2bb591a8930d177fa6de6c
Author: Nilesh Patra <nilesh@debian.org>
Date:   Sun Jul 31 18:49:33 2022 +0000

    Attempt building on more archs
    
    It doesn't seem to work on arm64 as of yet, log below.
    Don't know why it triggers bolt again, but * sigh *
    
    ./bolt \
        --bfile=EUR_subset \
        --phenoFile=EUR_subset.pheno2.covars \
        --exclude=EUR_subset.exclude2 \
        --phenoCol=PHENO \
        --phenoCol=QCOV1 \
        --modelSnps=EUR_subset.modelSnps2 \
        --reml \
        --numThreads=2
                          +-----------------------------+
                          |                       ___   |
                          |   BOLT-LMM, v2.3.6   /_ /   |
                          |   October 29, 2021    /_/   |
                          |   Po-Ru Loh            //   |
                          |                        /    |
                          +-----------------------------+
    
    Copyright (C) 2014-2021 Harvard University.
    Distributed under the GNU GPLv3 open source license.
    
    Boost version: 1_74
    
    Command line options:
    
    ./bolt \
        --bfile=EUR_subset \
        --phenoFile=EUR_subset.pheno2.covars \
        --exclude=EUR_subset.exclude2 \
        --phenoCol=PHENO \
        --phenoCol=QCOV1 \
        --modelSnps=EUR_subset.modelSnps2 \
        --reml \
        --numThreads=2
    
    Setting number of threads to 2
    fam: EUR_subset.fam
    bim(s): EUR_subset.bim
    bed(s): EUR_subset.bed
    
    === Reading genotype data ===
    
    Total indivs in PLINK data: Nbed = 379
    Total indivs stored in memory: N = 379
    Reading bim file #1: EUR_subset.bim
        Read 54051 snps
    Total snps in PLINK data: Mbed = 54051
    Reading exclude file (SNPs to exclude): EUR_subset.exclude2
    Excluded 47959 SNP(s)
    Reading list of SNPs to include in model (i.e., GRM): EUR_subset.modelSnps2
    WARNING: SNP has been excluded: rs2176153
    WARNING: SNP has been excluded: rs77036651
    WARNING: SNP has been excluded: rs189917831
    WARNING: SNP has been excluded: rs76452819
    WARNING: SNP has been excluded: rs77203822
    Included 1331 SNP(s) in model in 2 variance component(s)
    WARNING: 10420 SNP(s) had been excluded
    
    Breakdown of SNP pre-filtering results:
      1331 SNPs to include in model (i.e., GRM)
      0 additional non-GRM SNPs loaded
      52720 excluded SNPs
    Allocating 1331 x 380/4 bytes to store genotypes
    Reading genotypes and performing QC filtering on snps and indivs...
    Reading bed file #1: EUR_subset.bed
        Expecting 5134845 (+3) bytes for 379 indivs, 54051 snps
    Total indivs after QC: 379
    Total post-QC SNPs: M = 1331
      Variance component 1: 660 post-QC SNPs (name: 'chr21')
      Variance component 2: 671 post-QC SNPs (name: 'chr22')
    Time for SnpData setup = 0.630153 sec
    
    === Reading phenotype and covariate data ===
    
    Read data for 373 indivs (ignored 0 without genotypes) from:
      EUR_subset.pheno2.covars
    Number of indivs with no missing phenotype(s) to use: 369
    NOTE: Using all-1s vector (constant term) in addition to specified covariates
        Using quantitative covariate: CONST_ALL_ONES
    Number of individuals used in analysis: Nused = 369
    Singular values of covariate matrix:
        S[0] = 19.2094
    Total covariate vectors: C = 1
    Total independent covariate vectors: Cindep = 1
    
    === Initializing Bolt object: projecting and normalizing SNPs ===
    
    Number of chroms with >= 1 good SNP: 2
    Average norm of projected SNPs:           368.000000
    Dimension of all-1s proj space (Nused-1): 368
    Time for covariate data setup + Bolt initialization = 0.0125201 sec
    
    Phenotype 1:   N = 369   mean = -0.000706532   std = 1.02606
    Phenotype 2:   N = 369   mean = 1.53117   std = 0.499705
    
    === Estimating variance parameters ===
    
    === Making initial guesses for phenotype 1 ===
    
    Using 3 random trials
    
                          +-----------------------------+
                          |                       ___   |
                          |   BOLT-LMM, v2.3.6   /_ /   |
                          |   October 29, 2021    /_/   |
                          |   Po-Ru Loh            //   |
                          |                        /    |
                          +-----------------------------+
    
    Copyright (C) 2014-2021 Harvard University.
    Distributed under the GNU GPLv3 open source license.
    
    Boost version: 1_74
    
    Command line options:
    
    (null)
    
    ERROR: Use exactly one of the --bfile, --bfilegz, or --fam,bim,bed input formats
    Aborting due to error processing command line arguments
    For list of arguments, run with -h (--help) option