I cannot perform joint genotype calling using gVCFs using the GenotypeGVCF command on my dataset containing 352 mtDNA samples.
Does any one has run into this problem before, or has suggestions on how to get this working.
I have attached the standard output for a hanging run.
I can generate VCF files individually no problems.
INFO 17:06:45,732 GenomeAnalysisEngine - Strictness is SILENT INFO 17:06:45,867 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 17:06:47,721 MicroScheduler - Running the GATK in parallel mode with 4 total threads, 1 CPU thread(s) for each of 4 data thread(s), of 20 processors available on this machine INFO 17:06:47,791 GenomeAnalysisEngine - Preparing for traversal INFO 17:06:47,793 GenomeAnalysisEngine - Done preparing for traversal INFO 17:06:47,794 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 17:06:47,794 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 17:06:47,795 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 17:06:48,436 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files INFO 17:07:17,800 ProgressMeter - gi|251831106|ref|NC_012920.1|:1 0.0 30.0 s 49.6 w 0.0% 15250.3 w 15250.3 w Waiting for data... (interrupt to abort)
GATK VERSION: The Genome Analysis Toolkit (GATK) v3.4-0-g7e26428, Compiled 2015/05/15 03:25:41
java version "1.7.0_51"
Thanks for your time.