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Mutect2 ERROR: Null qss lines in bcbio log

mchimentimchimenti United StatesMember

Hi, I'm running bcbio mutect2 tumor/normal somatic variant calling on a linux cluster environment. I had to restart my job owing to an error in the bcbio config file (*.yaml), and upon editing the config file and restarting, I noticed that the pipeline began producing a lot (thousands) of these errors in the log:

[2017-01-19T22:28Z] INFO 16:28:45,687 ProgressMeter - 20:33587180 2.678151017E9 2.5 h 3.0 s 51.0% 4.9 h 2.4 h
[2017-01-19T22:28Z] INFO 16:28:46,114 ProgressMeter - 2:179499339 7.0449077071E10 11.3 h 0.0 s 73.3% 15.4 h 4.1 h
[2017-01-19T22:28Z] ERROR 16:28:47,438 MuTect2 - Null qss at 45506621
[2017-01-19T22:28Z] ERROR 16:28:48,223 MuTect2 - Null qss at 102394233
[2017-01-19T22:28Z] ERROR 16:28:48,411 MuTect2 - Null qss at 81919065

Before restarting, there were no (or few) errors. I tried searching for documentation about the meaning and causes of this error, but could not find anything except one github post saying not to worry about it. Any advice would be appreciated.

Here is an example mutect2 command being run by bcbio from the command log:

[2017-01-19T22:29Z] java -Xms681m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/Shared/Bioinformatics/data/mchiment/hansen_vs_exomes/bcbio_var2_mutect2_jan2017/work/mutect2/3/tx/tmpVAfsfP -jar /Shared/Bioinformatics/data/bcbio/toolplus/gatk/3.6-0-g89b7209/GenomeAnalysisTK.jar -T MuTect2 -R /Shared/Bioinformatics/data/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation ClippingRankSumTest --annotation DepthPerSampleHC --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I:tumor /Shared/Bioinformatics/data/mchiment/hansen_vs_exomes/bcbio_var2_mutect2_jan2017/work/bamprep/X3/3/X3-sort-3_0_198022430-prep.bam -I:normal /Shared/Bioinformatics/data/mchiment/hansen_vs_exomes/bcbio_var2_mutect2_jan2017/work/bamprep/X1/3/X1-sort-3_0_198022430-prep.bam -L /Shared/Bioinformatics/data/mchiment/hansen_vs_exomes/bcbio_var2_mutect2_jan2017/work/mutect2/3/X-3_0_198022430-regions-nolcr.bed --interval_set_rule INTERSECTION -ploidy 2 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment | bgzip -c > /Shared/Bioinformatics/data/mchiment/hansen_vs_exomes/bcbio_var2_mutect2_jan2017/work/mutect2/3/tx/tmpVAfsfP/X-3_0_198022430.vcf.gz

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @mchimenti
    Hi,

    Indeed those errors are nothing to worry about. They are just letting you know that the QSS annotation could not be annotated for those sites. QSS is the sum of base quality scores for each allele.

    -Sheila

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