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GenotypeGVCFs Hangs at the start

srynearson1srynearson1 Member
edited March 2016 in Ask the GATK team

Hi team, thanks for your work.

I'm currently running GenotypeGVCF on 78 WG individuals using the -L option to run each chromosome separately.

java -jar -Xmx20g -XX:ParallelGCThreads=10 
-Djava.io.tmpdir=/scratch/local/ GenomeAnalysisTK.jar 
-T GenotypeGVCFs
-R references/human_g1k_v37_decoy.fasta 
--disable_auto_index_creation_and_locking_when_reading_rods 
--num_threads 10
--variant [78 WG individuals]
--variant ...
 -L chr10_region.interval

I started running v3.0, but also ran v3.3, with the same issue.

Issue:

Each time it runs it gets to the same point and then hangs for >18 hours, before I kill the job.

INFO  09:57:47,938 HelpFormatter - Executing as me@kingspeak20 on Linux 2.6.32-504.30.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_85-mockbuild_2015_07_25_13_10-b00.
INFO  09:57:47,939 HelpFormatter - Date/Time: 2016/03/10 09:57:47
INFO  09:57:47,939 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:57:47,940 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:57:48,441 GenomeAnalysisEngine - Strictness is SILENT
INFO  09:57:48,661 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000

If I'm correct 78 WG individuals should not be an issue.

Any ideas as to what is causing this issue?

--Thanks

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