Error from running VBID2 after installing from source

[poloarol]

Hello!

I have been able to install VerifyBamID2 from source and tried to run, but keeping getting this error:

Initialize from FullLLKFunc(int dim, ContaminationEstimator* contPtr)

This is after I run this command:

VERIFY_BAM_ID_HOME=/home/user/software/VerifyBamID

root_path=/home/user/skills_test_3
bamfile=${root_path}/data/input/HGDP00082.GRCh38.low_coverage.cram
pileup_file=${root_path}/data/input/HGDP00082.GRCh38.low_coverage.pileup
outputfolder=${root_path}/data/output
out_pileup_file=${root_path}/data/output/HGDP00082.GRCh38.low_coverage.pileup
hg38=${root_path}/reference/GRCh38_full_analysis_set_plus_decoy_hla.fa
svd=${VERIFY_BAM_ID_HOME}/resource/1000g.100k.b38.vcf.gz.dat

${VERIFY_BAM_ID_HOME}/bin/VerifyBamID \
    --SVDPrefix ${svd} \
    --PileupFile ${pileup_file} \
    --Reference ${hg38} \
    --BamFile ${bamfile} \
    --Output ${outputfolder} \
    --UDPath ${svd}.UD \
    --MeanPath ${svd}.mu \
    --BedPath ${svd}.bed \
    --NumPC 4

This is the output log:

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

 Version:2.0.1
 Copyright (c) 2009-2020 by Hyun Min Kang and Fan Zhang
 This project is licensed under the terms of the MIT license.

The following parameters are available.  Ones with "[]" are in effect:

Available Options
                    Input/Output Files : --BamFile [/home/user/skills_test_3/data/input/HGDP00082.GRCh38.low_coverage.cram],
                                         --PileupFile [/home/user/skills_test_3/data/input/HGDP00082.GRCh38.low_coverage.pileup],
                                         --Reference [/home/user/skills_test_3/reference/GRCh38_full_analysis_set_plus_decoy_hla.fa],
                                         --SVDPrefix [/home/user/software/VerifyBamID/resource/1000g.100k.b38.vcf.gz.dat],
                                         --Output [/home/user/skills_test_3/data/output]
               Model Selection Options : --WithinAncestry,
                                         --DisableSanityCheck, --NumPC [4],
                                         --FixPC [Empty],
                                         --FixAlpha [-1.0e+00],
                                         --KnownAF [Empty], --NumThread [4],
                                         --Seed [12345], --Epsilon [1.0e-08],
                                         --OutputPileup, --Verbose
   Construction of SVD Auxiliary Files : --RefVCF [Empty]
                        Pileup Options : --min-BQ [13], --min-MQ [2],
                                         --adjust-MQ [40], --max-depth [8000],
                                         --no-orphans, --incl-flags [1040],
                                         --excl-flags [1796]
                    Deprecated Options : --UDPath [/home/user/software/VerifyBamID/resource/1000g.100k.b38.vcf.gz.dat.UD],
                                         --MeanPath [/home/user/software/VerifyBamID/resource/1000g.100k.b38.vcf.gz.dat.mu],
                                         --BedPath [/home/user/software/VerifyBamID/resource/1000g.100k.b38.vcf.gz.dat.bed]

Initialize from FullLLKFunc(int dim, ContaminationEstimator* contPtr)

Any help would be appreciated.

Thanks

[Griffan]

Hi @poloarol, thanks for reporting the issue, this message is just a log message, not an error message. Do you mean the process finished without generating any results?

BTW, the --BamFile and --PileipFile input should be mutually exclusive, you don't need to specify both of them.

[poloarol]

@Griffan I got it work. Thanks for the explanation.

I will close the issue.