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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
UnifiedGenotyper queue extension
Johan_Dahlberg
✭✭✭Member ✭✭✭
It says in the "ExampleUnifiedGenotyper" qscript that it runs an incomplete version of the UnifiedGenotyper. I have a two questions about this.
- I cannot find the org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper class, is this not in the public source or am I blind?
- Does the "incomplete" in the script starting comment mean that this extension is incomplete in its functionality? Or is it something else that is incomplete in its nature?
Basically I'm wondering if there are any pitfalls for me if I start using the example script as a base for my own variant calling qscript.
Best Answer
-
kshakir
✭✭ ✭✭
Most of the queue.extensions are generated classes once you run 'ant'. The generated classes are Queue compatible versions of the walker command arguments. Instead of looking at the generated scala file you can find the same or better argument descriptions in the the gatkdocs for each walker.
The 'incomplete' status of the script means that it is only a technical example, and will need to be tweaked for your specific requirements in your calling pipeline. Feel free to explore different command line options with the UG. For example using Queue you can create two instances of the UG and test using with BAQ and without. As for what UG commands you should be using, see the UG gatkdocs and the Best Practices for an overall description of where the UG fits in a calling pipeline.
Answers
Most of the queue.extensions are generated classes once you run 'ant'. The generated classes are Queue compatible versions of the walker command arguments. Instead of looking at the generated scala file you can find the same or better argument descriptions in the the gatkdocs for each walker.
The 'incomplete' status of the script means that it is only a technical example, and will need to be tweaked for your specific requirements in your calling pipeline. Feel free to explore different command line options with the UG. For example using Queue you can create two instances of the UG and test using with BAQ and without. As for what UG commands you should be using, see the UG gatkdocs and the Best Practices for an overall description of where the UG fits in a calling pipeline.
Thank you! That cleared things up for me.
I also cannot find the UnifiedGenotyper class, and I have ran ant. Classes for other walkers are there. Does this class even exist or it is just mentioned as an example?
@armen, can you tell me a bit more about what you are trying to do and what problem you are experiencing?
Hi @Geraldine_VdAuwera,
I followed the instructions on http://gatkforums.broadinstitute.org/discussion/1309/queue-with-intellij-idea to setup Queue with IntelliJ, and I'm trying to edit the example Unified Genotyper script public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala. However, the IDE tells me that the class UnifiedGenotyper doesn't exist.
If I run ExampleUnifiedGenotyper.scala using Queue:
java -jar dist/Queue.jar -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala -help
I get errors for the same reason:
INFO 16:31:27,906 QScriptManager - Compiling 1 QScript
ERROR 16:31:29,701 QScriptManager - ExampleUnifiedGenotyper.scala:73: not found: type UnifiedGenotyper
ERROR 16:31:29,706 QScriptManager - val genotyper = new UnifiedGenotyper with UnifiedGenotyperArguments
ERROR 16:31:29,706 QScriptManager - ^
ERROR 16:31:29,906 QScriptManager - ExampleUnifiedGenotyper.scala:78: value scatterCount is not a member of AnyRef with ExampleUnifiedGenotyper.this.UnifiedGenotyperArguments
ERROR 16:31:29,909 QScriptManager - genotyper.scatterCount = 3
ERROR 16:31:29,909 QScriptManager - ^
ERROR 16:31:30,245 QScriptManager - ExampleUnifiedGenotyper.scala:80: value out is not a member of AnyRef with ExampleUnifiedGenotyper.this.UnifiedGenotyperArguments
ERROR 16:31:30,247 QScriptManager - genotyper.out = swapExt(qscript.bamFile, "bam", "unfiltered.vcf")
ERROR 16:31:30,248 QScriptManager - ^
ERROR 16:31:30,279 QScriptManager - ExampleUnifiedGenotyper.scala:82: value out is not a member of AnyRef with ExampleUnifiedGenotyper.this.UnifiedGenotyperArguments
ERROR 16:31:30,281 QScriptManager - evalUnfiltered.eval :+= genotyper.out
ERROR 16:31:30,282 QScriptManager - ^
ERROR 16:31:30,319 QScriptManager - ExampleUnifiedGenotyper.scala:83: value out is not a member of AnyRef with ExampleUnifiedGenotyper.this.UnifiedGenotyperArguments
ERROR 16:31:30,321 QScriptManager - evalUnfiltered.out = swapExt(genotyper.out, "vcf", "eval")
ERROR 16:31:30,323 QScriptManager - ^
ERROR 16:31:30,354 QScriptManager - ExampleUnifiedGenotyper.scala:85: value out is not a member of AnyRef with ExampleUnifiedGenotyper.this.UnifiedGenotyperArguments
ERROR 16:31:30,356 QScriptManager - variantFilter.variant = genotyper.out
ERROR 16:31:30,356 QScriptManager - ^
ERROR 16:31:30,441 QScriptManager - 6 errors found
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
org.broadinstitute.sting.queue.QException: Compile of public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala failed with 6 errors
at org.broadinstitute.sting.queue.QScriptManager.loadScripts(QScriptManager.scala:71)
at org.broadinstitute.sting.queue.QCommandLine.org$broadinstitute$sting$queue$QCommandLine$$qScriptPluginManager(QCommandLine.scala:95)
at org.broadinstitute.sting.queue.QCommandLine.getArgumentSources(QCommandLine.scala:227)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:202)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.7-1-g9092aa6):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Compile of public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala failed with 6 errors
ERROR ------------------------------------------------------------------------------------------
INFO 16:31:30,601 QCommandLine - Shutting down jobs. Please wait...
I'm getting the same error. If I checkout the git repository and build using ant, I'm unable to find the GATK extensions. However, the prebuilt version of Queue works fine.
Just for more clarifications...the Piccard extensions work fine and I cloned the repo on Monday.
Hi folks, two quick questions to help find out what the problem is:
Are you running
ant cleanbefore building? Sometimes justantisn't enough.What is the output of the command:
jar tvf dist/Queue.jar | grep 'extensions/gatk'?I also tried git checkout tags/2.6 followed by ant clean and ant queue. The error persists. It might be ivy related?
Same results for me.
Based on the output you attached, it looks like you're building from our "GATK framework only" repository (https://github.com/broadgsa/gatk) instead of our full "framework + tools" repository (https://github.com/broadgsa/gatk-protected), which includes both the core framework as well as our flagship tools like the UnifiedGenotyper and the HaplotypeCaller. In order to use the UnifiedGenotyper with Queue you'll need to clone and build from the gatk-protected repository.
Hope this helps,
David
Gotcha, thanks!
Thank you @droazen, it works now!
It would be helpful to put the link to the full repository in http://gatkforums.broadinstitute.org/discussion/1306/overview-of-queue.
@armen, I'll add the link. Thanks for the suggestion!