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Picard 2.10.2 is now available at https://github.com/broadinstitute/picard/releases.
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Picard's CollectMultipleMetrics in Queue v3.4 and v3.5

brisk022brisk022 University of ZurichMember
in Ask the GATK team

Greetings,

Some of the picard's collect (e.g. CollectMultipleMetrics, CollectInsertSizeMetrics) commands load R script resources. Those resources were present in Queue <= v3.3-0 but they are absent from the subsequent versions.
$ jar tf 3.3-0/Queue.jar | grep "picard.*R$" picard/analysis/baseDistributionByCycle.R picard/analysis/gcBias.R picard/analysis/meanQualityByCycle.R picard/analysis/rnaSeqCoverage.R picard/analysis/qualityScoreDistribution.R picard/analysis/insertSizeHistogram.R $ jar tf 3.4-0/Queue.jar | grep "picard.*R$" $ jar tf 3.5-0/Queue.jar | grep "picard.*R$" $
Without those resources, CollectMultipleMetrics throws something similar to java.lang.IllegalArgumentException: Script [picard/analysis/qualityScoreDistribution.R] not found in classpath depending on which commands it hits first. I thought I would be able to overcome that by adding picard.jar to CLASSPATH but it did not help. I had to add them to Queue.jar in order to make it work.

It would be nice to have those resources back in the distributed Queue.jar.

Thanks!

Roman

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Issue · Github
by Sheila

Issue Number
407
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    It looks like the June issue was something different; unfortunately it's not clear what's going wrong and we don't have the resources to address this at this time. If someone external figures it out and submits a patch we're happy to look at it of course. Sorry to disappoint!

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  • brisk022brisk022 University of ZurichMember

    Thanks for looking into that, Geraldine. Unfortunately, I don't have much experience with Maven, so I wouldn't be of much help.

    PS Do you give badges to people for reporting the most obscure issues? ;)

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hah, sure! Have a Trophy badge :)

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