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GenotypeGVCFs stuck at Starting traversal for coulple of days!!!
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Bug Report
Affected tool(s) or class(es)
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ate of test?]
Description
Describe the problem below. Provide screenshots , stacktrace , logs where appropriate. GenotypeGVCFs stuck at Starting traversal for coulple of days:
Using GATK jar /public/software/apps/gatk/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx50G -Djava.io.tmpdir=./tmp -jar /public/software/apps/gatk/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar GenotypeGVCFs -R /public/home/gaoshibin/B73_REF/Zea_mays.AGPv4.dna.toplevel.fa -V gendb://./CHR4_gvcf_database -G StandardAnnotation -O fat_ALL_MATERIALS_chr4.g.vcf.gz 11:58:13.194 WARN GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardAnnotation) is enabled for this tool by default 11:58:14.522 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/public/software/apps/gatk/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 20, 2022 11:58:19 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 11:58:19.059 INFO GenotypeGVCFs - ------------------------------------------------------------ 11:58:19.060 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.9.0 11:58:19.060 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 11:58:19.060 INFO GenotypeGVCFs - Executing as gaoshibin@fat1 on Linux v3.10.0-693.el7.x86_64 amd64 11:58:19.060 INFO GenotypeGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_211-b12 11:58:19.060 INFO GenotypeGVCFs - Start Date/Time: 2022年5月20日 上午11时58分13秒 11:58:19.060 INFO GenotypeGVCFs - ------------------------------------------------------------ 11:58:19.060 INFO GenotypeGVCFs - ------------------------------------------------------------ 11:58:19.061 INFO GenotypeGVCFs - HTSJDK Version: 2.23.0 11:58:19.061 INFO GenotypeGVCFs - Picard Version: 2.23.3 11:58:19.061 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 11:58:19.061 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 11:58:19.061 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 11:58:19.061 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 11:58:19.061 INFO GenotypeGVCFs - Deflater: IntelDeflater 11:58:19.061 INFO GenotypeGVCFs - Inflater: IntelInflater 11:58:19.062 INFO GenotypeGVCFs - GCS max retries/reopens: 20 11:58:19.062 INFO GenotypeGVCFs - Requester pays: disabled 11:58:19.062 INFO GenotypeGVCFs - Initializing engine 11:58:27.760 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.3.2-e18fa63 12:26:28.692 info NativeGenomicsDB - pid=228304 tid=228306 No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records 12:26:28.734 info NativeGenomicsDB - pid=228304 tid=228306 No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records 12:26:28.734 info NativeGenomicsDB - pid=228304 tid=228306 No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records 12:57:29.524 INFO GenotypeGVCFs - Done initializing engine 12:57:32.773 INFO ProgressMeter - Starting traversal 12:57:32.773 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
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Feature request
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Description
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@Bowen1992 Could you please try running with the latest GATK release (4.2.6.1) and reporting whether the issue persists?
I tried the latest GATK release and also reported errors. Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx50G -Djava.io.tmpdir=./tmp -jar /public/home/gaoshibin/software/GATK/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar GenotypeGVCFs -R /public/home/gaoshibin/B73_REF/Zea_mays.AGPv4.dna.toplevel.fa -V gendb://./CHR7_gvcf_database -G StandardAnnotation --genomicsdb-shared-posixfs-optimizations true -O new_ALL_MATERIALS_chr7.g.vcf.gz 17:49:50.404 WARN GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardAnnotation) is enabled for this tool by default 17:49:50.653 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/public/home/gaoshibin/software/GATK/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so 17:49:51.271 INFO GenotypeGVCFs - ------------------------------------------------------------ 17:49:51.273 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.2.6.1 17:49:51.273 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 17:49:51.273 INFO GenotypeGVCFs - Executing as gaoshibin@comput6 on Linux v3.10.0-693.el7.x86_64 amd64 17:49:51.274 INFO GenotypeGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_211-b12 17:49:51.274 INFO GenotypeGVCFs - Start Date/Time: 2022年5月22日 下午05时49分50秒 17:49:51.274 INFO GenotypeGVCFs - ------------------------------------------------------------ 17:49:51.275 INFO GenotypeGVCFs - ------------------------------------------------------------ 17:49:51.276 INFO GenotypeGVCFs - HTSJDK Version: 2.24.1 17:49:51.276 INFO GenotypeGVCFs - Picard Version: 2.27.1 17:49:51.276 INFO GenotypeGVCFs - Built for Spark Version: 2.4.5 17:49:51.277 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 17:49:51.277 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 17:49:51.277 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 17:49:51.277 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 17:49:51.278 INFO GenotypeGVCFs - Deflater: IntelDeflater 17:49:51.278 INFO GenotypeGVCFs - Inflater: IntelInflater 17:49:51.278 INFO GenotypeGVCFs - GCS max retries/reopens: 20 17:49:51.278 INFO GenotypeGVCFs - Requester pays: disabled 17:49:51.278 INFO GenotypeGVCFs - Initializing engine 17:49:52.385 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.4.3-6069e4a 17:52:35.478 info NativeGenomicsDB - pid=66560 tid=66565 No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records 17:52:35.487 info NativeGenomicsDB - pid=66560 tid=66565 No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records 17:52:35.487 info NativeGenomicsDB - pid=66560 tid=66565 No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records 17:55:56.179 INFO GenotypeGVCFs - Done initializing engine 17:55:56.692 INFO ProgressMeter - Starting traversal 17:55:56.704 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 07:43:39.738 INFO ProgressMeter - 7:1067 2267.7 1000 0.4 07:44:22.642 INFO ProgressMeter - 7:2069 2268.4 2000 0.9 07:45:48.820 INFO GenotypeGVCFs - Shutting down engine GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6.764015676999995,Cpu time(s),6.525572708 [2022年5月24日 上午07时45分51秒] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 2,276.03 minutes. Runtime.totalMemory()=2278555648 java.lang.IllegalStateException: Genotype has no likelihoods: [CAU-SICAU-Y1035 A*/T GQ 80 DP 10] at org.broadinstitute.hellbender.utils.GenotypeUtils.computeDiploidGenotypeCounts(GenotypeUtils.java:89) at org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet.calculateEH(ExcessHet.java:96) at org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet.annotate(ExcessHet.java:84) at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.addInfoAnnotations(VariantAnnotatorEngine.java:355) at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:334) at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:306) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.regenotypeVC(GenotypeGVCFsEngine.java:185) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.callRegion(GenotypeGVCFsEngine.java:135) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.apply(GenotypeGVCFs.java:283) at org.broadinstitute.hellbender.engine.VariantLocusWalker.lambda$traverse$0(VariantLocusWalker.java:135) at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEachOrdered(ReferencePipeline.java:423) at org.broadinstitute.hellbender.engine.VariantLocusWalker.traverse(VariantLocusWalker.java:132) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289)
@Bowen1992 Could you please try running with the latest GATK release (
4.2.6.1) and reporting whether the issue persists?
Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx50G -Djava.io.tmpdir=./tmp -jar /public/home/gaoshibin/software/GATK/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar GenotypeGVCFs -R /public/home/gaoshibin/B73_REF/Zea_mays.AGPv4.dna.toplevel.fa -V gendb://./CHR7_gvcf_database -G StandardAnnotation --genomicsdb-shared-posixfs-optimizations true -O new_ALL_MATERIALS_chr7.g.vcf.gz 17:49:50.404 WARN GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardAnnotation) is enabled for this tool by default 17:49:50.653 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/public/home/gaoshibin/software/GATK/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so 17:49:51.271 INFO GenotypeGVCFs - ------------------------------------------------------------ 17:49:51.273 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.2.6.1 17:49:51.273 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 17:49:51.273 INFO GenotypeGVCFs - Executing as gaoshibin@comput6 on Linux v3.10.0-693.el7.x86_64 amd64 17:49:51.274 INFO GenotypeGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_211-b12 17:49:51.274 INFO GenotypeGVCFs - Start Date/Time: 2022年5月22日 下午05时49分50秒 17:49:51.274 INFO GenotypeGVCFs - ------------------------------------------------------------ 17:49:51.275 INFO GenotypeGVCFs - ------------------------------------------------------------ 17:49:51.276 INFO GenotypeGVCFs - HTSJDK Version: 2.24.1 17:49:51.276 INFO GenotypeGVCFs - Picard Version: 2.27.1 17:49:51.276 INFO GenotypeGVCFs - Built for Spark Version: 2.4.5 17:49:51.277 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 17:49:51.277 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 17:49:51.277 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 17:49:51.277 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 17:49:51.278 INFO GenotypeGVCFs - Deflater: IntelDeflater 17:49:51.278 INFO GenotypeGVCFs - Inflater: IntelInflater 17:49:51.278 INFO GenotypeGVCFs - GCS max retries/reopens: 20 17:49:51.278 INFO GenotypeGVCFs - Requester pays: disabled 17:49:51.278 INFO GenotypeGVCFs - Initializing engine 17:49:52.385 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.4.3-6069e4a 17:52:35.478 info NativeGenomicsDB - pid=66560 tid=66565 No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records 17:52:35.487 info NativeGenomicsDB - pid=66560 tid=66565 No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records 17:52:35.487 info NativeGenomicsDB - pid=66560 tid=66565 No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records 17:55:56.179 INFO GenotypeGVCFs - Done initializing engine 17:55:56.692 INFO ProgressMeter - Starting traversal 17:55:56.704 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 07:43:39.738 INFO ProgressMeter - 7:1067 2267.7 1000 0.4 07:44:22.642 INFO ProgressMeter - 7:2069 2268.4 2000 0.9 07:45:48.820 INFO GenotypeGVCFs - Shutting down engine GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6.764015676999995,Cpu time(s),6.525572708 [2022年5月24日 上午07时45分51秒] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 2,276.03 minutes. Runtime.totalMemory()=2278555648 java.lang.IllegalStateException: Genotype has no likelihoods: [CAU-SICAU-Y1035 A*/T GQ 80 DP 10] at org.broadinstitute.hellbender.utils.GenotypeUtils.computeDiploidGenotypeCounts(GenotypeUtils.java:89) at org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet.calculateEH(ExcessHet.java:96) at org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet.annotate(ExcessHet.java:84) at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.addInfoAnnotations(VariantAnnotatorEngine.java:355) at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:334) at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:306) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.regenotypeVC(GenotypeGVCFsEngine.java:185) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.callRegion(GenotypeGVCFsEngine.java:135) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.apply(GenotypeGVCFs.java:283) at org.broadinstitute.hellbender.engine.VariantLocusWalker.lambda$traverse$0(VariantLocusWalker.java:135) at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEachOrdered(ReferencePipeline.java:423) at org.broadinstitute.hellbender.engine.VariantLocusWalker.traverse(VariantLocusWalker.java:132) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289)
@Bowen1992 I got the same error, do you have a solution now?
Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx76800m -jar /home/zwc1988/miniconda3/envs/gatk/share/gatk4-4.2.6.1-0/gatk-package-4.2.6.1-local.jar GenotypeGVCFs -R data/ref/CL200105941_L02.fa -V gendb://results/genotype/genodb/group2 -O results/genotype/vcfs/group2.vcf.gz --tmp-dir ./tmp 18:24:10.205 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/zwc1988/miniconda3/envs/gatk/share/gatk4-4.2.6.1-0/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so 18:24:10.451 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:24:10.452 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.2.6.1 18:24:10.452 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 18:24:10.452 INFO GenotypeGVCFs - Executing as zwc1988@fat01 on Linux v3.10.0-957.el7.x86_64 amd64 18:24:10.453 INFO GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_312-b07 18:24:10.453 INFO GenotypeGVCFs - Start Date/Time: June 19, 2022 6:24:10 PM CST 18:24:10.453 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:24:10.453 INFO GenotypeGVCFs - ------------------------------------------------------------ 18:24:10.454 INFO GenotypeGVCFs - HTSJDK Version: 2.24.1 18:24:10.454 INFO GenotypeGVCFs - Picard Version: 2.27.1 18:24:10.454 INFO GenotypeGVCFs - Built for Spark Version: 2.4.5 18:24:10.454 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 18:24:10.455 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 18:24:10.455 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 18:24:10.455 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 18:24:10.455 INFO GenotypeGVCFs - Deflater: IntelDeflater 18:24:10.455 INFO GenotypeGVCFs - Inflater: IntelInflater 18:24:10.455 INFO GenotypeGVCFs - GCS max retries/reopens: 20 18:24:10.455 INFO GenotypeGVCFs - Requester pays: disabled 18:24:10.456 INFO GenotypeGVCFs - Initializing engine 18:24:13.851 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.4.3-6069e4a 18:24:15.434 info NativeGenomicsDB - pid=225671 tid=225691 No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records 18:24:15.434 info NativeGenomicsDB - pid=225671 tid=225691 No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records 18:24:15.434 info NativeGenomicsDB - pid=225671 tid=225691 No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records 18:24:15.434 info NativeGenomicsDB - pid=225671 tid=225691 No valid combination operation found for INFO field AC - the field will NOT be part of INFO fields in the generated VCF records 18:24:15.434 info NativeGenomicsDB - pid=225671 tid=225691 No valid combination operation found for INFO field AF - the field will NOT be part of INFO fields in the generated VCF records 18:24:15.434 info NativeGenomicsDB - pid=225671 tid=225691 No valid combination operation found for INFO field AN - the field will NOT be part of INFO fields in the generated VCF records 18:24:15.434 info NativeGenomicsDB - pid=225671 tid=225691 No valid combination operation found for INFO field FS - the field will NOT be part of INFO fields in the generated VCF records 18:24:15.435 info NativeGenomicsDB - pid=225671 tid=225691 No valid combination operation found for INFO field QD - the field will NOT be part of INFO fields in the generated VCF records 18:24:15.435 info NativeGenomicsDB - pid=225671 tid=225691 No valid combination operation found for INFO field SOR - the field will NOT be part of INFO fields in the generated VCF records 18:24:22.489 INFO GenotypeGVCFs - Done initializing engine 18:24:24.770 INFO ProgressMeter - Starting traversal 18:24:24.771 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 18:25:30.829 INFO GenotypeGVCFs - Shutting down engine GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.055026962999999963,Cpu time(s),0.049579712000000026 [June 19, 2022 6:25:30 PM CST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 1.35 minutes. Runtime.totalMemory()=3063414784 java.lang.IllegalStateException: Genotype has no likelihoods: [10 G/G GQ 15 DP 5] at org.broadinstitute.hellbender.utils.GenotypeUtils.computeDiploidGenotypeCounts(GenotypeUtils.java:89) at org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet.calculateEH(ExcessHet.java:96) at org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet.annotate(ExcessHet.java:84) at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.addInfoAnnotations(VariantAnnotatorEngine.java:355) at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:334) at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:306) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.regenotypeVC(GenotypeGVCFsEngine.java:185) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.callRegion(GenotypeGVCFsEngine.java:135) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.apply(GenotypeGVCFs.java:283) at org.broadinstitute.hellbender.engine.VariantLocusWalker.lambda$traverse$0(VariantLocusWalker.java:135) at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEachOrdered(ReferencePipeline.java:490) at org.broadinstitute.hellbender.engine.VariantLocusWalker.traverse(VariantLocusWalker.java:132) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289)
