INFO 12:09:23,863 HelpFormatter - -------------------------------------------------------------------------------- INFO 12:09:23,865 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22 INFO 12:09:23,865 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 12:09:23,866 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 12:09:23,869 HelpFormatter - Program Args: -T GenotypeGVCFs -R /scratch/ucgd/serial/u0413537/UGP_Pipeline_Data/references/human_g1k_v37_decoy.fasta --num_threads 20 --variant /scratch/local/NA12880.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12879.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12886.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12882.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12889.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12885.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12877.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12878.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12892.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12884.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12887.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12888.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12893.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12883.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12890.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12881.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/NA12891.gatk.raw.snps.indels.gCat.vcf --variant /scratch/local/FIN_mergeGvcf.vcf --variant /scratch/local/GBR_mergeGvcf.vcf --variant /scratch/local/CEU_mergeGvcf.vcf -L /scratch/kingspeak/serial/u0413537/Platinum/UGP_Pipeline_Results/chr1_region_file.list -o /scratch/kingspeak/serial/u0413537/Platinum/UGP_Pipeline_Results/chr1_region_genotyped.vcf INFO 12:09:23,880 HelpFormatter - Executing as u0413537@kp179 on Linux 2.6.32-358.18.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_75-mockbuild_2015_01_08_20_32-b00. INFO 12:09:23,880 HelpFormatter - Date/Time: 2015/03/17 12:09:23 INFO 12:09:23,880 HelpFormatter - -------------------------------------------------------------------------------- INFO 12:09:23,880 HelpFormatter - -------------------------------------------------------------------------------- INFO 12:09:23,997 GenomeAnalysisEngine - Strictness is SILENT INFO 12:09:24,081 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 12:09:46,318 IntervalUtils - Processing 249250621 bp from intervals INFO 12:09:46,345 MicroScheduler - Running the GATK in parallel mode with 20 total threads, 1 CPU thread(s) for each of 20 data thread(s), of 40 processors available on this machine INFO 12:09:46,529 GenomeAnalysisEngine - Preparing for traversal INFO 12:09:46,533 GenomeAnalysisEngine - Done preparing for traversal INFO 12:09:46,534 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 12:09:46,534 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 12:09:46,535 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 12:09:46,722 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files WARN 12:10:12,060 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:19203155 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:10:20,257 ProgressMeter - 1:19205801 0.0 33.0 s 55.8 w 7.7% 7.1 m 6.6 m WARN 12:10:34,088 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:19315151 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:10:34,095 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:19315215 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:10:44,439 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:19516806 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:10:50,417 ProgressMeter - 1:19594401 0.0 63.0 s 105.6 w 7.9% 13.4 m 12.3 m WARN 12:11:01,300 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:19689754 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:11:22,186 ProgressMeter - 1:19812001 0.0 95.0 s 158.2 w 7.9% 19.9 m 18.3 m WARN 12:11:23,574 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:19867720 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:12:05,843 ProgressMeter - 1:19999901 0.0 2.3 m 230.3 w 8.0% 28.9 m 26.6 m WARN 12:12:18,803 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:6087279 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:13:05,980 ProgressMeter - 1:19999901 1000000.0 3.3 m 3.3 m 8.0% 41.3 m 38.0 m INFO 12:13:37,489 ProgressMeter - 1:19999901 1000000.0 3.8 m 3.8 m 8.0% 47.8 m 43.9 m WARN 12:14:01,208 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:2295244 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:14:01,564 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:4556963 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:14:01,569 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:4556990 has 12 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:14:02,626 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:6793250 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:14:03,427 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:4603763 has 17 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:14:03,551 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:6828013 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:14:04,972 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:6850435 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:14:07,490 ProgressMeter - 1:19999901 1000000.0 4.3 m 4.3 m 8.0% 54.0 m 49.7 m WARN 12:14:15,844 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:4895092 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:14:17,605 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:4945625 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:14:17,670 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:4948380 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:14:42,206 ProgressMeter - 1:19999901 3000000.0 4.9 m 98.0 s 8.0% 61.3 m 56.4 m WARN 12:15:01,749 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:15438825 has 13 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:15:06,217 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:12368705 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:15:08,260 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:15520071 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:15:09,725 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:15556050 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:15:09,855 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:15562109 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:15:12,381 ProgressMeter - 1:19999901 3000000.0 5.4 m 108.0 s 8.0% 67.5 m 62.1 m INFO 12:16:09,549 ProgressMeter - 1:19999901 3000000.0 6.4 m 2.1 m 8.0% 79.6 m 73.2 m WARN 12:16:11,786 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:12677525 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:16:21,483 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:12849547 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:16:33,116 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:18043268 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:16:39,789 ProgressMeter - 1:19999901 4000000.0 6.9 m 103.0 s 8.0% 85.8 m 78.9 m WARN 12:17:01,352 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:18442336 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:17:02,866 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:18503886 has 12 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:17:03,535 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:18534891 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:17:03,912 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:18551579 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:17:10,930 ProgressMeter - 1:19999901 5000000.0 7.4 m 88.0 s 8.0% 92.2 m 84.8 m WARN 12:17:16,703 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:18812478 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:17:19,559 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:20199272 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:18:55,646 ProgressMeter - 1:20235701 6000000.0 9.2 m 91.0 s 8.1% 112.7 m 103.6 m INFO 12:20:10,738 ProgressMeter - 1:20237601 6000000.0 10.4 m 104.0 s 8.1% 2.1 h 117.7 m INFO 12:21:06,910 ProgressMeter - 1:20239101 6000000.0 11.3 m 113.0 s 8.1% 2.3 h 2.1 h INFO 12:21:59,451 ProgressMeter - 1:20270001 6000000.0 12.2 m 2.0 m 8.1% 2.5 h 2.3 h INFO 12:22:54,651 ProgressMeter - 1:20290701 6000000.0 13.1 m 2.2 m 8.1% 2.7 h 2.5 h INFO 12:23:28,759 ProgressMeter - 1:20315401 6000000.0 13.7 m 2.3 m 8.2% 2.8 h 2.6 h INFO 12:24:55,693 ProgressMeter - 1:20369401 6000000.0 15.2 m 2.5 m 8.2% 3.1 h 2.8 h WARN 12:24:55,866 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:9163163 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:25:46,974 ProgressMeter - 1:20394401 6000000.0 16.0 m 2.7 m 8.2% 3.3 h 3.0 h INFO 12:27:09,609 ProgressMeter - 1:20417201 6000000.0 17.4 m 2.9 m 8.2% 3.5 h 3.2 h WARN 12:27:20,673 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:7344186 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 12:27:20,678 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:7344237 has 12 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:28:34,041 ProgressMeter - 1:20434301 6000000.0 18.8 m 3.1 m 8.2% 3.8 h 3.5 h INFO 12:29:47,647 ProgressMeter - 1:20439001 6000000.0 20.0 m 3.3 m 8.2% 4.1 h 3.7 h INFO 12:30:26,495 ProgressMeter - 1:20444601 6000000.0 20.7 m 3.4 m 8.2% 4.2 h 3.9 h WARN 12:30:26,753 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:9263597 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:31:01,304 ProgressMeter - 1:20470001 6000000.0 21.2 m 3.5 m 8.2% 4.3 h 4.0 h INFO 12:32:17,245 ProgressMeter - 1:20474601 6000000.0 22.5 m 3.8 m 8.2% 4.6 h 4.2 h WARN 12:32:38,612 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:7458253 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:32:54,064 ProgressMeter - 1:20476101 6000000.0 23.1 m 3.9 m 8.2% 4.7 h 4.3 h INFO 12:33:34,611 ProgressMeter - 1:20481401 6000000.0 23.8 m 4.0 m 8.2% 4.8 h 4.4 h INFO 12:34:14,088 ProgressMeter - 1:20496701 6000000.0 24.5 m 4.1 m 8.2% 5.0 h 4.5 h INFO 12:35:40,625 ProgressMeter - 1:20501601 6000000.0 25.9 m 4.3 m 8.2% 5.2 h 4.8 h INFO 12:37:08,376 ProgressMeter - 1:22001901 6000000.0 27.4 m 4.6 m 8.8% 5.2 h 4.7 h INFO 12:38:21,315 ProgressMeter - 1:22004701 6000000.0 28.6 m 4.8 m 8.8% 5.4 h 4.9 h INFO 12:39:34,924 ProgressMeter - 1:22005001 6000000.0 29.8 m 5.0 m 8.8% 5.6 h 5.1 h INFO 12:40:40,546 ProgressMeter - 1:22005401 6000000.0 30.9 m 5.2 m 8.8% 5.8 h 5.3 h INFO 12:41:19,299 ProgressMeter - 1:22005701 6000000.0 31.5 m 5.3 m 8.8% 6.0 h 5.4 h INFO 12:42:02,884 ProgressMeter - 1:22007901 6000000.0 32.3 m 5.4 m 8.8% 6.1 h 5.6 h INFO 12:42:42,975 ProgressMeter - 1:22013601 6000000.0 32.9 m 5.5 m 8.8% 6.2 h 5.7 h WARN 12:42:43,002 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:8022800 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:44:13,487 ProgressMeter - 1:22015301 7000000.0 34.4 m 4.9 m 8.8% 6.5 h 5.9 h INFO 12:44:47,885 ProgressMeter - 1:22018701 7000000.0 35.0 m 5.0 m 8.8% 6.6 h 6.0 h INFO 12:45:36,966 ProgressMeter - 1:22023701 7000000.0 35.8 m 5.1 m 8.8% 6.8 h 6.2 h INFO 12:46:10,028 ProgressMeter - 1:22027601 7000000.0 36.4 m 5.2 m 8.8% 6.9 h 6.3 h INFO 12:46:43,196 ProgressMeter - 1:22030001 7000000.0 36.9 m 5.3 m 8.8% 7.0 h 6.3 h WARN 12:46:43,218 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:22030120 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:47:18,973 ProgressMeter - 1:22030701 7000000.0 37.5 m 5.4 m 8.8% 7.1 h 6.5 h INFO 12:47:50,965 ProgressMeter - 1:22032201 7000000.0 38.1 m 5.4 m 8.8% 7.2 h 6.5 h INFO 12:48:24,088 ProgressMeter - 1:22033101 7000000.0 38.6 m 5.5 m 8.8% 7.3 h 6.6 h INFO 12:48:57,160 ProgressMeter - 1:22034801 7000000.0 39.2 m 5.6 m 8.8% 7.4 h 6.7 h INFO 12:49:30,119 ProgressMeter - 1:22035401 7000000.0 39.7 m 5.7 m 8.8% 7.5 h 6.8 h WARN 12:49:41,008 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:20531561 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 12:50:03,286 ProgressMeter - 1:22039301 7000000.0 40.3 m 5.8 m 8.8% 7.6 h 6.9 h INFO 12:50:36,713 ProgressMeter - 1:22041901 7000000.0 40.8 m 5.8 m 8.8% 7.7 h 7.0 h INFO 12:51:10,054 ProgressMeter - 1:22044201 7000000.0 41.4 m 5.9 m 8.8% 7.8 h 7.1 h INFO 12:51:42,852 ProgressMeter - 1:22047001 7000000.0 41.9 m 6.0 m 8.8% 7.9 h 7.2 h INFO 12:53:32,673 ProgressMeter - 1:22047501 7000000.0 43.8 m 6.3 m 8.8% 8.2 h 7.5 h INFO 12:54:31,355 ProgressMeter - 1:22047501 7000000.0 44.7 m 6.4 m 8.8% 8.4 h 7.7 h INFO 12:55:52,276 ProgressMeter - 1:22048001 7000000.0 46.1 m 6.6 m 8.8% 8.7 h 7.9 h INFO 12:57:12,152 ProgressMeter - 1:22048101 7000000.0 47.4 m 6.8 m 8.8% 8.9 h 8.1 h ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.RuntimeException: java.lang.reflect.InvocationTargetException at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:189) at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:336) at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.attemptToLockAndLoadIndexFromDisk(RMDTrackBuilder.java:320) at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:279) at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:225) at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:148) at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createNewResource(ReferenceOrderedDataSource.java:226) at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createNewResource(ReferenceOrderedDataSource.java:185) at org.broadinstitute.gatk.engine.datasources.rmd.ResourcePool.iterator(ResourcePool.java:84) at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.seek(ReferenceOrderedDataSource.java:168) at org.broadinstitute.gatk.engine.datasources.providers.RodLocusView.(RodLocusView.java:83) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.getLocusView(TraverseLociNano.java:129) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:80) 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:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.GeneratedConstructorAccessor29.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:526) at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:185) ... 18 more Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded at htsjdk.tribble.index.interval.IntervalTreeIndex$ChrIndex.read(IntervalTreeIndex.java:202) at htsjdk.tribble.index.AbstractIndex.read(AbstractIndex.java:363) at htsjdk.tribble.index.interval.IntervalTreeIndex.(IntervalTreeIndex.java:50) ... 22 more INFO 12:58:32,300 ProgressMeter - 1:22048201 7000000.0 48.8 m 7.0 m 8.8% 9.2 h 8.4 h ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af): ##### 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 http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: java.lang.reflect.InvocationTargetException ##### ERROR ------------------------------------------------------------------------------------------