The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at http://bit.ly/2i4mGxz

Picard's CollectMultipleMetrics in Queue v3.4 and v3.5

brisk022brisk022 University of ZurichMember Posts: 11 ✭✭✭

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

Issue · Github
by Sheila

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

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,118 admin

    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!

    Geraldine Van der Auwera, PhD

  • brisk022brisk022 University of ZurichMember Posts: 11 ✭✭✭

    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? ;)

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,118 admin

    Hah, sure! Have a Trophy badge :)

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.