We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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
-
Geraldine_VdAuwera
Cambridge, MA admin
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