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Picard's CollectMultipleMetrics in Queue v3.4 and v3.5
brisk022
University of ZurichMember
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
Best Answer
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Geraldine_VdAuwera
Cambridge, MAMember, Administrator, Broadie
Hi @brisk022, I'm not sure why these resources are no longer loading correctly; they are part of the Picard jar that gets wrapped into Queue at build time and they haven't been moved in Picard afaict -- but I have a faint memory of running into a similar problem some time last June. I'll try to hunt down what might have happened.
Answers
Hi @brisk022, I'm not sure why these resources are no longer loading correctly; they are part of the Picard jar that gets wrapped into Queue at build time and they haven't been moved in Picard afaict -- but I have a faint memory of running into a similar problem some time last June. I'll try to hunt down what might have happened.
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!
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?
Hah, sure! Have a Trophy badge