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UCSF-Costello-Lab / LG3_Pipeline

The original LG3 pipeline
https://github.com/UCSF-Costello-Lab/LG3_Pipeline
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WARN: undefined variables MQRankSum and ReadPosRankSum #160

Open HenrikBengtsson opened 2 years ago

HenrikBengtsson commented 2 years ago

Investigate the following by going back to earlier version to see if this is recently introduced or something that has always been there:

$ lg3 --version
2020-05-26-9000 (commit cb09e9f)

$ grep -E "(ERR|WARN).*undefined" _Recal_Patient157t10.out | head
WARN  23:14:56,389 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum 
WARN  23:14:56,391 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum 
WARN  23:14:56,401 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum 
WARN  23:14:56,401 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum 
WARN  23:14:56,404 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum 
WARN  23:14:56,405 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum 
WARN  23:14:56,407 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum 
WARN  23:14:56,408 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum 
WARN  23:14:56,421 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum 
WARN  23:14:56,422 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
HenrikBengtsson commented 2 years ago

I just tested with lg3 2019-03-23, and this is there too:

$ lg3 --version
2019-03-23 (commit 749df93)

$ grep -E "(ERR|WARN).*undefined" _Recal_Patient157t10.out | head
WARN  15:04:39,054 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum 
WARN  15:04:39,056 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum 
WARN  15:04:39,063 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum 
WARN  15:04:39,064 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum 
WARN  15:04:39,066 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum 
WARN  15:04:39,066 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum 
WARN  15:04:39,069 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum 
WARN  15:04:39,070 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum 
WARN  15:04:39,073 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum 
WARN  15:04:39,073 Interpreter - org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.initializeMatchExps@314![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
HenrikBengtsson commented 2 years ago

@ivan108, these WARNINGs goes back to at least 2019-03-23. Do you have a sense whether or not these are important? I think they originate from:

https://github.com/UCSF-Costello-Lab/LG3_Pipeline/blob/3a3688b827b2b540b46864901ed96e03f525cdb6/scripts/Germline.sh#L172-L175