Question: Unified Genotyper Error CloudMap
gravatar for miles.william.mee
3.8 years ago by
miles.william.mee10 wrote:

I'm trying to run the workflow "Cloudmap: Unmapped mutant Worflow_3-6-2014". The step  "Unified Genotyper" is returning an error and stopping the workflow. I have tried running "Unified Genotyper" with the setting "Genotype likelihoods calculation model to employ" set to BOTH, SNP and INDEL  separately. It will successfully run when set to SNP but will return the same error message when set to either BOTH or INDEL . Does anyone know why this isn't working?

Picked up _JAVA_OPTIONS:
[Mon Feb 02 15:11:13 CST 2015] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/galaxy-repl/main/scratch/tmp-gatk-n2c6mk/gatk_input.fasta OUTPUT=/galaxy-repl/main/scratch/tmp-gatk-n2c6mk/dict1299450959375208537.tmp    TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon Feb 02 15:11:13 CST 2015] Executing as on Linux 2.6.32-504.8.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_40-b43; Picard version: 1.58(1057)
[Mon Feb 02 15:11:14 CST 2015] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.02 minutes.
##### ERROR ------------------------------------------------------------------------------------------
##### 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(
	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 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(
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version exported):
##### 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 wiki for extensive documentation
##### ERROR Visit our forum to view answers to commonly asked questions
##### ERROR
##### ERROR MESSAGE: Index: 0, Size: 0
##### ERROR ------------------------------------------------------------------------------------------
unified genotyper • 1.4k views
ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson25k • written 3.8 years ago by miles.william.mee10
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The error comes up when this specific GATK tool runs out of memory to complete the job. It is linked to the options you mention, in all cases that I have seen. Sometimes not using BOTH will work to reduce the job resource load, but not always, as in your case.

You may be able to adjust other parameters on the tool form to lower the memory usage, but in most cases you will need to move to a cloud Galaxy where more dedicated resource can be allocated (by you).

More about this type of error in general is here in our wiki:

Best, Jen, Galaxy team

ADD COMMENTlink written 3.8 years ago by Jennifer Hillman Jackson25k

Hi Jen,

Could I download the files that would have been used for this step and input them into a local instillation of GATK on my computer to just do that step, then upload the output files to use in the rest of the workflow?


Miles Mee

ADD REPLYlink written 3.8 years ago by miles.william.mee10

Hi Miles, You can try that, but your local computer must have enough memory to process the job. How much is needed will depend on the data inputs. Using a Custom Reference Genome increases the resources needed by the job. Do double check that you are providing a ROD file when using the Indel option, as that can be a contributing issue for certain cases. A ticket to track this issue on Main is below. The decision is whether to allocate more resource, if that is actually the root cause of the problem and not just what came out of my initial testing:

Click on "Tutorial" in the top menu here in Galaxy Biostars and review post for "Get Galaxy" to learn more about starting up a local Galaxy.

Thanks, Jen

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Jennifer Hillman Jackson25k
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