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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 [email protected] 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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