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Error when running own walker

DavyK1984DavyK1984 Posts: 5Member
edited February 2013 in Ask the GATK team

Hi All, In my desparate attempts to learn more about how the GATK works, but since it's written in JAVA, which I have almost no clue about (python all the way), so to be honest I've not the faintest idea how to go about troubleshooting the below error.

I found a blog post by the ever wonderful Pierre Lindebaum here that went through compiling and running you're first GATK walker.

First using Pierre's example (after some compiling issues as there doesn't seem to be a ReadMetaDataTracker class anymore and I replace with RefMetaDataTracker) I get the following error:

java -cp /path/to/GenomeAnalysisTK.jar:/path/to/cofoja-1.0-r139.jar:/path/to/HelloRead.jar org.broadinstitute.sting.gatk.CommandLineGATK -T HelloRead -I path/to/test.bam -R /path/to/human_g1k_v37.fasta
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.NullPointerException
    at org.broadinstitute.sting.utils.classloader.JVMUtils.isAnonymous(JVMUtils.java:91)
    at org.broadinstitute.sting.utils.classloader.PluginManager.<init>(PluginManager.java:155)
    at org.broadinstitute.sting.utils.classloader.PluginManager.<init>(PluginManager.java:124)
    at org.broadinstitute.sting.gatk.WalkerManager.<init>(WalkerManager.java:55)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.<init>(GenomeAnalysisEngine.java:160)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.<init>(CommandLineExecutable.java:53)
    at org.broadinstitute.sting.gatk.CommandLineGATK.<init>(CommandLineGATK.java:57)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.2-16-g9f648cb):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, 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: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------

I thought that was a very strange error and in Pierre's example he used GATK version 1.4 where as I am on 2.2.

I also tried the following

java -cp /path/to/cofoja-1.0-r139.jar:/path/to/HelloRead.jar -jar /path/to/GenomeAnalysisTK.jar -T HelloRead -I path/to/test.bam -R /path/to/human_g1k_v37.fasta
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.2-16-g9f648cb): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: HelloRead
##### ERROR ------------------------------------------------------------------------------------------

I have not tried downloading on older version of the GATK and running it with that. I'm pretty much stuck here. Any help is greatly appreciated.

Cheers, Davy

Post edited by DavyK1984 on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,295Administrator, GATK Developer admin

    Hi Davy,

    Unfortunately we don't currently provide support for development, and anyway without seeing your code I couldn't really say what's wrong. I'll see if I can get Pierre to comment on here since it's his instructions you're following, he might have some useful insights.

    I'll just add that the version difference may result in a number of Pierre's instructions needing to be adapted. I would strongly recommend taking the time to figure out what adaptations need to be made rather than revert to the older version, because we have made significant improvements to the framework since then. You really don't want to be stuck in the past.

    Also, some more general advice is that you should maybe try to learn some java skills by working on a simple standalone dummy project before tackling the GATK. I come from Python originally so I understand the culture shock; many things that you know how to do in Python require a very different approach in java. It can take a little time and practice to get comfortable with that. One thing you may find it very useful would be to figure out how to debug java code.

    Good luck!

    Geraldine Van der Auwera, PhD

  • DavyK1984DavyK1984 Posts: 5Member

    Thanks for the advice Geraldine. Off the find a decent java tutorial :(

  • lindenblindenb Posts: 5Member

    @DavyK1984 thank you for the "wornderful" :-) I'm sorry that my code doesn't work anymore with the newest versions of the GATK. Unfortunately I'm too lazy to go back to my code (although my code worked I had not idea about a software that would do its job using only one Walker).

  • DavyK1984DavyK1984 Posts: 5Member

    It's ok. I've resigned my self to learning java. Probably for the best.

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