Question: Issue with Unified Genotyper
0
gravatar for viviane.laine
3.8 years ago by
France
viviane.laine0 wrote:

Hi,

I get an issue while running the workflow "Cloudmap: Unmapped mutant Worflow_3-6-2014". The workflow stops at the step "Unified Genotyper". I've tried to rerun it several times, but it still doesn't work while several weeks ago it was working correctly. I'm using default settings and I got the following error message:

##### ERROR stack trace 
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.rangeCheck(Unknown Source)
	at java.util.ArrayList.get(Unknown Source)
	at net.sf.samtools.Cigar.getCigarElement(Cigar.java:54)
	at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.computeReadHaplotypeLikelihoods(PairHMMIndelErrorModel.java:441)
	at org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel.getLikelihoods(IndelGenotypeLikelihoodsCalculationModel.java:392)
	at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoods(UnifiedGenotyperEngine.java:246)
	at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:184)
	at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:276)
	at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:112)
	at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78)
	at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
	at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:63)
	at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:233)
	at  org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122)
	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
	at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:90)

Does anyone have a suggestion? Many thanks!

gatk unifiedgenotyper cloudmap • 1.5k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by viviane.laine0
1
gravatar for Wolfgang Maier
3.8 years ago by
Germany
Wolfgang Maier590 wrote:

Hi Viviane,

I do not know why things have stopped working (has the installed version of the GATK genotyper changed recently ?), but to get the workflow fixed you may want to contact its author, Gregory Minevich, directly.

What I can also tell you is that we have developed MiModD, a piece of software which can do all the upstream steps  of mapping and variant calling similar to what's included in the CloudMap workflow for you on your local computer.

It runs on Mac and Linux machines provided they have enough memory. Enough depends on the genome of the organism you are working with, but in case you want to analyze C. elegans data 8 GB are sufficient.
MiModD can produce output ready to be fed into the CloudMap Hawaiian and other Mapping tools so you can bypass the whole rest of the workflow.

You can use it as a command line tool or from within a local Galaxy installation. The latest release can be found at  https://sourceforge.net/projects/mimodd and there is a manual (though incomplete still) at http://mimodd.readthedocs.org .

If you are interested, tell me which OS you would use and whether you are experienced with command line tools and I could suggest an installation mode that suits your needs.

Best,

Wolfgang

ADD COMMENTlink written 3.8 years ago by Wolfgang Maier590
0
gravatar for viviane.laine
3.8 years ago by
France
viviane.laine0 wrote:

Hi Wolfgang,

Thanks for your answer, but unfortunately, I'm using Windows machine, and I'm not familiar with command line tools.

As far as Unified Genotyper is concerned, it seems the tool is not working, indepentently from the Cloudmap workflow: I tried to make the tool run but it stops with the same error message.

Any idea?

Thanks

 

ADD COMMENTlink written 3.8 years ago by viviane.laine0
0
gravatar for Wolfgang Maier
3.8 years ago by
Germany
Wolfgang Maier590 wrote:

Well going through the Java traceback the error seems to occur with some calculations for indels.

In the right side bar there is a related post HELP! A Runtime Error in Running Unified Genotyper where Jennifer Hillman Jackson points out an issue when the tool is used with "Genotype likelihoods calculation model to employ:" set to BOTH.

Maybe that is your issue and you can just set it to SNP ? For the workflow, of course, other changes may be required then.

Best,

Wolfgang

ADD COMMENTlink written 3.8 years ago by Wolfgang Maier590
0
gravatar for viviane.laine
3.8 years ago by
France
viviane.laine0 wrote:

Thank you very much, it's now working! I run the tool independently with each setting (SNP or INDEL) and then I combine the files. It's two more steps but, well, it's working!

Thank you for your help,

Viviane

ADD COMMENTlink written 3.8 years ago by viviane.laine0
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