Hello!
I would like to run GenotypeGVCFs on 209 WES, called with HC (--emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000).
When I run GenotypeGVCFs, with this command (computing nodes have 8 cores and 24G of memory) :
java -Xmx24g -jar $GATK_JAR \
-R Homo_sapiens.GRCh37_decoy.fa \
-T GenotypeGVCFs \
-nt 8 \
-V gvcf.all.list \
-o calls.vcf
It estimates a huge runtime and just dies hanging:
INFO 10:27:00,790 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:27:00,795 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO 10:27:00,796 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 10:27:00,796 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 10:27:00,800 HelpFormatter - Program Args: -R Homo_sapiens.GRCh37_decoy.fa -T GenotypeGVCFs -nt 8 -V gvcf.all.list -o calls.vcf
INFO 10:27:00,810 HelpFormatter - Executing as emixaM@r107-n50 on Linux 2.6.32-504.12.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_60-ea-b07.
INFO 10:27:00,810 HelpFormatter - Date/Time: 2015/03/19 10:27:00
INFO 10:27:00,811 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:27:00,811 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:27:04,719 GenomeAnalysisEngine - Strictness is SILENT
INFO 10:27:04,882 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 10:27:41,565 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 1 CPU thread(s) for each of 8 data thread(s), of 8 processors available on this machine
INFO 10:27:43,169 GenomeAnalysisEngine - Preparing for traversal
INFO 10:27:43,179 GenomeAnalysisEngine - Done preparing for traversal
INFO 10:27:43,179 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 10:27:43,180 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 10:27:43,180 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 10:27:44,216 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
INFO 10:28:15,035 ProgressMeter - 1:1000201 0.0 31.0 s 52.7 w 0.0% 27.0 h 27.0 h
INFO 10:29:17,386 ProgressMeter - 1:1068701 0.0 94.0 s 155.8 w 0.0% 76.7 h 76.6 h
INFO 10:30:18,055 ProgressMeter - 1:1115101 0.0 2.6 m 256.1 w 0.0% 5.0 d 5.0 d
What did I do wrong?
Cheers!