Error when running own walker
Posted in Ask the team | Last updated on 2013-02-01 10:32:52


Comments (4)

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


Return to top Comment on this article in the forum