GenotypeGVCF crashes ?

sabqsabq UppsalaMember

For what a reason the GenotypeGVCFs crashes at the same position on chr4 (only for chr4). below is the error message. any hint on this ? thanks

LSBATCH: User input

java -Xmx64g -Djava.io.tmpdir=/home/ChrGVCF/tmp -jar /usr/users/GenomeAnalysisTK.jar -T GenotypeGVCFs -R /home/gVCF/ref.fa -V Chr4.list -o /home/vcf/Chr4.vcf --dbsnp /usr/users/gVCF/vcf.gz -stand_call_conf 10 -stand_emit_conf 10

Exited with exit code 1.

Resource usage summary:

CPU time :                                   3092.37 sec.
Max Memory :                                 21023 MB
Average Memory :                             13545.71 MB
Total Requested Memory :                     -
Delta Memory :                               -
Max Swap :                                   -
Max Processes :                              3
Max Threads :                                29
Run time :                                   2858 sec.
Turnaround time :                            2868 sec.

The output (if any) follows:

INFO 16:40:59,584 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:40:59,586 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 16:40:59,586 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 16:40:59,586 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 16:40:59,590 HelpFormatter - Program Args: -T GenotypeGVCFs -R /home/gVCF/ref.fa -V Chr4.list -o /home/vcf/Chr4.vcf --dbsnp /usr/users/gVCF/vcf.gz -stand_call_conf 10 -stand_emit_conf 10
INFO 16:40:59,600 HelpFormatter - Executing as [email protected] on Linux 3.10.0-327.36.3.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_111-mockbuild_2016_07_27_06_39-b00.
INFO 16:40:59,600 HelpFormatter - Date/Time: 2017/01/16 16:40:59
INFO 16:40:59,600 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:40:59,601 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:41:06,974 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:41:07,790 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
WARN 16:54:48,682 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
INFO 16:54:48,864 GenomeAnalysisEngine - Preparing for traversal
INFO 16:54:48,904 GenomeAnalysisEngine - Done preparing for traversal
INFO 16:54:48,905 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 16:54:48,905 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 16:54:48,905 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
WARN 16:55:00,452 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.
WARN 16:55:00,453 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.
INFO 16:55:00,453 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
INFO 16:55:18,915 ProgressMeter - 1:52843733 1147176.0 30.0 s 26.0 s 5.0% 9.9 m 9.4 m
INFO 16:55:48,917 ProgressMeter - 1:144547777 3188081.0 60.0 s 18.0 s 13.8% 7.2 m 6.2 m
INFO 16:56:18,918 ProgressMeter - 12:1610786 5245795.0 90.0 s 17.0 s 22.6% 6.6 m 5.1 m
INFO 16:56:48,919 ProgressMeter - 18:7901055 7343457.0 120.0 s 16.0 s 30.5% 6.6 m 4.6 m
INFO 16:57:18,920 ProgressMeter - 2:77614744 9434763.0 2.5 m 15.0 s 39.1% 6.4 m 3.9 m
INFO 16:57:48,922 ProgressMeter - 21:5786231 1.1484734E7 3.0 m 15.0 s 47.9% 6.3 m 3.3 m
INFO 16:58:18,923 ProgressMeter - 3:51776128 1.3588051E7 3.5 m 15.0 s 56.1% 6.2 m 2.7 m
INFO 16:58:48,925 ProgressMeter - 32:35 1.4861718E7 4.0 m 16.0 s 61.7% 6.5 m 2.5 m
WARN 16:59:03,217 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs
WARN 16:59:04,416 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 4:434 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument. This warning message is output just once per run and further warnings will be suppressed unless the DEBUG logging level is used.
INFO 16:59:18,984 ProgressMeter - 4:24401 1.4861762E7 4.5 m 18.0 s 61.7% 7.3 m 2.8 m
INFO 16:59:49,204 ProgressMeter - 4:94301 1.4861762E7 5.0 m 20.0 s 61.7% 8.1 m 3.1 m
INFO 17:00:19,205 ProgressMeter - 4:158201 1.4861762E7 5.5 m 22.0 s 61.7% 8.9 m 3.4 m
INFO 17:00:49,206 ProgressMeter - 4:222001 1.4861762E7 6.0 m 24.0 s 61.7% 9.7 m 3.7 m
INFO 17:01:29,206 ProgressMeter - 4:305401 1.4861762E7 6.7 m 26.0 s 61.8% 10.8 m 4.1 m
INFO 17:01:59,207 ProgressMeter - 4:365301 1.4861762E7 7.2 m 28.0 s 61.8% 11.6 m 4.4 m
INFO 17:02:29,208 ProgressMeter - 4:427601 1.4861762E7 7.7 m 30.0 s 61.8% 12.4 m 4.7 m
INFO 17:02:59,209 ProgressMeter - 4:488701 1.4861762E7 8.2 m 32.0 s 61.8% 13.2 m 5.1 m
INFO 17:03:29,210 ProgressMeter - 4:547401 1.4861762E7 8.7 m 35.0 s 61.8% 14.0 m 5.4 m
INFO 17:04:09,211 ProgressMeter - 4:624801 1.4861762E7 9.3 m 37.0 s 61.8% 15.1 m 5.8 m
INFO 17:04:39,212 ProgressMeter - 4:682801 1.4861762E7 9.8 m 39.0 s 61.8% 15.9 m 6.1 m
INFO 17:05:19,213 ProgressMeter - 4:757601 1.4861762E7 10.5 m 42.0 s 61.8% 17.0 m 6.5 m
INFO 17:05:49,214 ProgressMeter - 4:813601 1.4861762E7 11.0 m 44.0 s 61.8% 17.8 m 6.8 m
INFO 17:06:19,215 ProgressMeter - 4:868001 1.4861762E7 11.5 m 46.0 s 61.8% 18.6 m 7.1 m
INFO 17:06:49,216 ProgressMeter - 4:922301 1.4861762E7 12.0 m 48.0 s 61.8% 19.4 m 7.4 m
INFO 17:07:19,217 ProgressMeter - 4:976901 1.4861762E7 12.5 m 50.0 s 61.8% 20.2 m 7.7 m
INFO 17:07:49,337 ProgressMeter - 4:1020601 1.5861762E7 13.0 m 49.0 s 61.8% 21.0 m 8.0 m
INFO 17:08:29,338 ProgressMeter - 4:1094401 1.5861762E7 13.7 m 51.0 s 61.8% 22.1 m 8.4 m
INFO 17:08:59,339 ProgressMeter - 4:1146801 1.5861762E7 14.2 m 53.0 s 61.8% 22.9 m 8.7 m
INFO 17:09:39,340 ProgressMeter - 4:1216401 1.5861762E7 14.8 m 56.0 s 61.8% 24.0 m 9.2 m
INFO 17:10:09,341 ProgressMeter - 4:1269301 1.5861762E7 15.3 m 58.0 s 61.8% 24.8 m 9.5 m
INFO 17:10:39,342 ProgressMeter - 4:1321201 1.5861762E7 15.8 m 59.0 s 61.9% 25.6 m 9.8 m
INFO 17:11:09,343 ProgressMeter - 4:1373501 1.5861762E7 16.3 m 61.0 s 61.9% 26.4 m 10.1 m
INFO 17:11:49,344 ProgressMeter - 4:1439901 1.5861762E7 17.0 m 64.0 s 61.9% 27.5 m 10.5 m
INFO 17:12:19,345 ProgressMeter - 4:1489201 1.5861762E7 17.5 m 66.0 s 61.9% 28.3 m 10.8 m
INFO 17:12:49,346 ProgressMeter - 4:1541401 1.5861762E7 18.0 m 68.0 s 61.9% 29.1 m 11.1 m
INFO 17:13:19,347 ProgressMeter - 4:1594601 1.5861762E7 18.5 m 70.0 s 61.9% 29.9 m 11.4 m
INFO 17:13:49,348 ProgressMeter - 4:1646401 1.5861762E7 19.0 m 71.0 s 61.9% 30.7 m 11.7 m
INFO 17:14:19,349 ProgressMeter - 4:1696701 1.5861762E7 19.5 m 73.0 s 61.9% 31.5 m 12.0 m
INFO 17:14:59,350 ProgressMeter - 4:1762701 1.5861762E7 20.2 m 76.0 s 61.9% 32.6 m 12.4 m
INFO 17:15:29,352 ProgressMeter - 4:1813701 1.5861762E7 20.7 m 78.0 s 61.9% 33.4 m 12.7 m
INFO 17:15:59,353 ProgressMeter - 4:1864501 1.5861762E7 21.2 m 80.0 s 61.9% 34.2 m 13.0 m
INFO 17:16:29,354 ProgressMeter - 4:1912801 1.5861762E7 21.7 m 81.0 s 61.9% 35.0 m 13.3 m
INFO 17:16:59,355 ProgressMeter - 4:1966501 1.5861762E7 22.2 m 83.0 s 61.9% 35.8 m 13.6 m
INFO 17:17:29,356 ProgressMeter - 4:2006201 1.6861762E7 22.7 m 80.0 s 61.9% 36.6 m 13.9 m
INFO 17:18:09,357 ProgressMeter - 4:2088901 1.6861762E7 23.3 m 83.0 s 61.9% 37.7 m 14.3 m
INFO 17:18:39,358 ProgressMeter - 4:2142401 1.6861762E7 23.8 m 84.0 s 61.9% 38.5 m 14.7 m
INFO 17:19:19,359 ProgressMeter - 4:2208001 1.6861762E7 24.5 m 87.0 s 61.9% 39.6 m 15.1 m
INFO 17:19:49,360 ProgressMeter - 4:2259101 1.6861762E7 25.0 m 88.0 s 61.9% 40.4 m 15.4 m
INFO 17:20:19,361 ProgressMeter - 4:2309301 1.6861762E7 25.5 m 90.0 s 61.9% 41.2 m 15.7 m
INFO 17:20:59,362 ProgressMeter - 4:2379901 1.6861762E7 26.2 m 93.0 s 62.0% 42.2 m 16.1 m
INFO 17:21:29,367 ProgressMeter - 4:2432801 1.6861762E7 26.7 m 94.0 s 62.0% 43.0 m 16.4 m
INFO 17:21:59,368 ProgressMeter - 4:2482901 1.6861762E7 27.2 m 96.0 s 62.0% 43.8 m 16.7 m
INFO 17:22:29,572 ProgressMeter - 4:2528601 1.6861762E7 27.7 m 98.0 s 62.0% 44.6 m 17.0 m
INFO 17:22:59,573 ProgressMeter - 4:2578301 1.6861762E7 28.2 m 100.0 s 62.0% 45.5 m 17.3 m
INFO 17:23:29,574 ProgressMeter - 4:2625701 1.6861762E7 28.7 m 102.0 s 62.0% 46.3 m 17.6 m
INFO 17:24:09,575 ProgressMeter - 4:2689201 1.6861762E7 29.3 m 104.0 s 62.0% 47.3 m 18.0 m
INFO 17:24:39,576 ProgressMeter - 4:2737501 1.6861762E7 29.8 m 106.0 s 62.0% 48.1 m 18.3 m
INFO 17:25:19,577 ProgressMeter - 4:2804301 1.6861762E7 30.5 m 108.0 s 62.0% 49.2 m 18.7 m
INFO 17:25:49,578 ProgressMeter - 4:2852401 1.6861762E7 31.0 m 110.0 s 62.0% 50.0 m 19.0 m
INFO 17:26:19,579 ProgressMeter - 4:2898301 1.6861762E7 31.5 m 112.0 s 62.0% 50.8 m 19.3 m
INFO 17:26:49,630 ProgressMeter - 4:2947001 1.6861762E7 32.0 m 113.0 s 62.0% 51.6 m 19.6 m
INFO 17:27:19,630 ProgressMeter - 4:2996301 1.6861762E7 32.5 m 115.0 s 62.0% 52.4 m 19.9 m
INFO 17:28:03,437 ProgressMeter - 4:3000201 1.7861762E7 33.2 m 111.0 s 62.0% 53.6 m 20.4 m
INFO 17:28:33,439 ProgressMeter - 4:3000201 1.7861762E7 33.7 m 113.0 s 62.0% 54.4 m 20.7 m

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NumberFormatException: For input string: ""
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:504)
at java.lang.Integer.valueOf(Integer.java:582)
at htsjdk.variant.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:717)
at htsjdk.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:128)
at htsjdk.variant.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:158)
at htsjdk.variant.variantcontext.LazyGenotypesContext.getGenotypes(LazyGenotypesContext.java:148)
at htsjdk.variant.variantcontext.GenotypesContext.getMaxPloidy(GenotypesContext.java:431)
at htsjdk.variant.variantcontext.VariantContext.getMaxPloidy(VariantContext.java:792)
at org.broadinstitute.gatk.tools.walkers.variantutils.ReferenceConfidenceVariantContextMerger.mergeRefConfidenceGenotypes(ReferenceConfidenceVariantContextMerger.java:422)
at org.broadinstitute.gatk.tools.walkers.variantutils.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:154)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:257)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:129)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
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: For input string: ""
ERROR ------------------------------------------------------------------------------------------
Tagged:

Answers

Sign In or Register to comment.