Question: GATK Runtime error - Avoid using deprecated tools or risk unexpected errors/results
gravatar for tammy.wiltshire
23 days ago by
tammy.wiltshire20 wrote:

Hi, I have successfully ran samples through the Galaxy pipeline, however, two samples have come up with an error when I run the unified genotyper. Hope someone can help, thank you

<h5>ERROR stack trace</h5>

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( at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.computeReadHaplotypeLikelihoods( at org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel.getLikelihoods( at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoods( at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes( at at at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse( at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse( at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute( at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute( at org.broadinstitute.sting.gatk.CommandLineExecutable.execute( at org.broadinstitute.sting.commandline.CommandLineProgram.start( at org.broadinstitute.sting.commandline.CommandLineProgram.start( at org.broadinstitute.sting.gatk.CommandLineGATK.main(

<h5>ERROR ------------------------------------------------------------------------------------------</h5> <h5>ERROR A GATK RUNTIME ERROR has occurred (version exported):</h5> <h5>ERROR</h5>
ADD COMMENTlink modified 22 days ago by Jennifer Hillman Jackson24k • written 23 days ago by tammy.wiltshire20
gravatar for Jennifer Hillman Jackson
22 days ago by
United States
Jennifer Hillman Jackson24k wrote:


All GATK tools wrapped for Galaxy, whether found on a public server, including Galaxy Main, or still available in the Main ToolShed are deprecated and should not be used. There is no active development planned for these older tool versions (related to the source licensing for these GATK versions). The latest GATK version has a more open usage license and the tools may be wrapped in the future by the IUC group (gitter chat) or other community contributors.

For Galaxy Main, these tools are pending an update to either hide or remove them entirely from the server:

The recommended workflow/tools for variant analysis are covered in the Galaxy tutorials (Freebayes and others).

Galaxy tutorial Hub:

Specifically, these tutorials are designed to work with the tools/resources at Galaxy Main:

  • Variant discovery: diploid case - this tutorial explains calling sequence variants in diploid systems like ... humans.
  • Variant discovery: haploid case - this tutorial explains calling sequence variants in haploid systems like ... bacteria and viruses.

More tutorials/guides are linked at the *Galaxy tutorial Hub * for use in a local/cloud/docker Galaxy that has been configured to include the tutorial's tools/resources. The Galaxy Training Network (GTN) site has details about the available pre-configured Docker Galaxy instances specific for tutorials plus other options -- direct link:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 22 days ago by Jennifer Hillman Jackson24k
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