Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

Help to run GenotypeGVCFs with 150 samples

First of all, thanks for GATK team.

I have 150 samples to analyze germline mutation. I already did Haplotypecaller GVCFmode.
But It might be too long to do GenotypeGVCFs. Thus, I used 'nt' but I got an error repeatedly.

A code is below and My server spec is 80cores and 750GB RAM.

java -Xmx256G -Djava.io.tmpdir=/data -jar 3-7-0-0/GenomeAnalysisTK.jar -T GenotypeGVCFs -R Homo_sapiens_hg19.fa --variant A.vcf --variant B.vcf ...... --variant C.vcf -nt 4 -o JointGenotype.vcf

INFO  17:16:28,301 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
WARN  17:16:30,301 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs
WARN  17:16:42,357 ExactAFCalculator - This tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr1: 54712 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument. Unless the DEBUG logging level is used, this warning message is output just once per run and further warnings are suppressed.
INFO  17:16:57,869 ProgressMeter -    chr1:1009601         0.0    30.0 s      49.6 w        0.0%    25.5 h      25.5 h
INFO  17:17:57,871 ProgressMeter -    chr1:2048101         0.0    90.0 s     148.8 w        0.1%    37.7 h      37.7 h
INFO  17:18:57,872 ProgressMeter -    chr1:3112401         0.0     2.5 m     248.0 w        0.1%    41.3 h      41.3 h
INFO  17:19:57,874 ProgressMeter -    chr1:3300501         0.0     3.5 m     347.2 w        0.1%    54.6 h      54.5 h
INFO  17:20:57,876 ProgressMeter -    chr1:3473301   1000000.0     4.5 m       4.5 m        0.1%    66.7 h      66.6 h
##### ERROR --
##### ERROR stack trace
java.util.ConcurrentModificationException
        at java.util.LinkedList$ListItr.checkForComodification(LinkedList.java:966)
        at java.util.LinkedList$ListItr.remove(LinkedList.java:921)
        at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.coveredByDeletion(GenotypingEngine.java:430)
        at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateOutputAlleleSubset(GenotypingEngine.java:387)
        at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:251)
        at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:392)
        at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:375)
        at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:330)
        at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:326)
        at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:304)
        at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:135)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
        at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
        at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
        at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------

What should I do for parallel computing ?
Thank you in advance.

Answers

Sign In or Register to comment.