Hi,
I am using gatk 4.0.8.1 HaplotypeCaller for making g.vcf. I am running follwing command
gatk --java-options "-Xms24g -Xmx48g" HaplotypeCaller -R new_hg38.fa -I S11_.sorted.BQRC.bam -O S11.g.vcf -L ../../nextera-dna-exome-targeted-regions-manifest-v1-2.bed --native-pair-hmm-threads 6 --min-base-quality-score 20 -stand-call-conf 30 --dbsnp /All_20180418.chr.hg38.vcf.gz -ERC GVCF -G StandardAnnotation -G AS_StandardAnnotation --read-validation-stringency SILENT --TMP_DIR scratch-2
But gatk is shutting down with exception.Here is log of exception
23:56:09.618 WARN GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardAnnotation) is enabled for this tool by default
23:56:09.692 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/hpcc/tools/gatk-4.0.8.1/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:56:10.099 INFO HaplotypeCaller - ------------------------------------------------------------
23:56:10.099 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.8.1
23:56:10.099 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
23:56:10.100 INFO HaplotypeCaller - Executing as hpcc@hpcc on Linux v4.4.0-159-generic amd64
23:56:10.100 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_222-8u222-b10-1ubuntu1~16.04.1-b10
23:56:10.100 INFO HaplotypeCaller - Start Date/Time: September 16, 2019 11:56:09 PM PKT
23:56:10.100 INFO HaplotypeCaller - ------------------------------------------------------------
23:56:10.100 INFO HaplotypeCaller - ------------------------------------------------------------
23:56:10.101 INFO HaplotypeCaller - HTSJDK Version: 2.16.0
23:56:10.101 INFO HaplotypeCaller - Picard Version: 2.18.7
23:56:10.101 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:56:10.101 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:56:10.102 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:56:10.102 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:56:10.102 INFO HaplotypeCaller - Deflater: IntelDeflater
23:56:10.102 INFO HaplotypeCaller - Inflater: IntelInflater
23:56:10.102 INFO HaplotypeCaller - GCS max retries/reopens: 20
23:56:10.102 INFO HaplotypeCaller - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX
23:56:10.102 INFO HaplotypeCaller - Initializing engine
23:56:10.936 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/2d6b1dc8-eccd-46f4-a5b2-39966cd786c9/data-base/All_20180418.chr.hg38.vcf.gz
23:56:11.249 INFO FeatureManager - Using codec BEDCodec to read file file:///mnt/2d6b1dc8-eccd-46f4-a5b2-39966cd786c9/scratch-2/exome-run2/cleanfastq/part3/newwork/../../nextera-dna-exome-targeted-regions-manifest-v1-2.bed
23:56:13.499 INFO IntervalArgumentCollection - Processing 45326818 bp from intervals
23:56:13.651 WARN IndexUtils - Feature file "/mnt/2d6b1dc8-eccd-46f4-a5b2-39966cd786c9/data-base/All_20180418.chr.hg38.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
23:56:14.042 INFO HaplotypeCaller - Shutting down engine
[September 16, 2019 11:56:14 PM PKT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=25739919360
java.lang.NullPointerException
at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:325)
at java.util.ComparableTimSort.sort(ComparableTimSort.java:202)
at java.util.Arrays.sort(Arrays.java:1312)
at java.util.Arrays.sort(Arrays.java:1506)
at java.util.ArrayList.sort(ArrayList.java:1462)
at java.util.Collections.sort(Collections.java:143)
at org.broadinstitute.hellbender.utils.IntervalUtils.sortAndMergeIntervals(IntervalUtils.java:459)
at org.broadinstitute.hellbender.utils.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:955)
at org.broadinstitute.hellbender.utils.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:970)
at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.<init>(MultiIntervalLocalReadShard.java:59)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.makeReadShards(AssemblyRegionWalker.java:195)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:175)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201)
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)
I am using gatk 4.0.8.1 HaplotypeCaller for making g.vcf. I am running follwing command
gatk --java-options "-Xms24g -Xmx48g" HaplotypeCaller -R new_hg38.fa -I S11_.sorted.BQRC.bam -O S11.g.vcf -L ../../nextera-dna-exome-targeted-regions-manifest-v1-2.bed --native-pair-hmm-threads 6 --min-base-quality-score 20 -stand-call-conf 30 --dbsnp /All_20180418.chr.hg38.vcf.gz -ERC GVCF -G StandardAnnotation -G AS_StandardAnnotation --read-validation-stringency SILENT --TMP_DIR scratch-2
But gatk is shutting down with exception.Here is log of exception
23:56:09.618 WARN GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardAnnotation) is enabled for this tool by default
23:56:09.692 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/hpcc/tools/gatk-4.0.8.1/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:56:10.099 INFO HaplotypeCaller - ------------------------------------------------------------
23:56:10.099 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.8.1
23:56:10.099 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
23:56:10.100 INFO HaplotypeCaller - Executing as hpcc@hpcc on Linux v4.4.0-159-generic amd64
23:56:10.100 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_222-8u222-b10-1ubuntu1~16.04.1-b10
23:56:10.100 INFO HaplotypeCaller - Start Date/Time: September 16, 2019 11:56:09 PM PKT
23:56:10.100 INFO HaplotypeCaller - ------------------------------------------------------------
23:56:10.100 INFO HaplotypeCaller - ------------------------------------------------------------
23:56:10.101 INFO HaplotypeCaller - HTSJDK Version: 2.16.0
23:56:10.101 INFO HaplotypeCaller - Picard Version: 2.18.7
23:56:10.101 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:56:10.101 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:56:10.102 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:56:10.102 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:56:10.102 INFO HaplotypeCaller - Deflater: IntelDeflater
23:56:10.102 INFO HaplotypeCaller - Inflater: IntelInflater
23:56:10.102 INFO HaplotypeCaller - GCS max retries/reopens: 20
23:56:10.102 INFO HaplotypeCaller - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX
23:56:10.102 INFO HaplotypeCaller - Initializing engine
23:56:10.936 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/2d6b1dc8-eccd-46f4-a5b2-39966cd786c9/data-base/All_20180418.chr.hg38.vcf.gz
23:56:11.249 INFO FeatureManager - Using codec BEDCodec to read file file:///mnt/2d6b1dc8-eccd-46f4-a5b2-39966cd786c9/scratch-2/exome-run2/cleanfastq/part3/newwork/../../nextera-dna-exome-targeted-regions-manifest-v1-2.bed
23:56:13.499 INFO IntervalArgumentCollection - Processing 45326818 bp from intervals
23:56:13.651 WARN IndexUtils - Feature file "/mnt/2d6b1dc8-eccd-46f4-a5b2-39966cd786c9/data-base/All_20180418.chr.hg38.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
23:56:14.042 INFO HaplotypeCaller - Shutting down engine
[September 16, 2019 11:56:14 PM PKT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=25739919360
java.lang.NullPointerException
at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:325)
at java.util.ComparableTimSort.sort(ComparableTimSort.java:202)
at java.util.Arrays.sort(Arrays.java:1312)
at java.util.Arrays.sort(Arrays.java:1506)
at java.util.ArrayList.sort(ArrayList.java:1462)
at java.util.Collections.sort(Collections.java:143)
at org.broadinstitute.hellbender.utils.IntervalUtils.sortAndMergeIntervals(IntervalUtils.java:459)
at org.broadinstitute.hellbender.utils.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:955)
at org.broadinstitute.hellbender.utils.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:970)
at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.<init>(MultiIntervalLocalReadShard.java:59)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.makeReadShards(AssemblyRegionWalker.java:195)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:175)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201)
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)