I am trying to run GATK HAPLOTYPECALLER and dit is crashing. Could someone help?
numactl -N 0 -m 0 /home/administrator/IGIB/gatk-4.1.4.0/gatk --java-options "-Xmx50g" HaplotypeCaller -R "/home/administrator/IGIB/samples/Homo_sapiens_assembly38.fasta" -I Sample_aligned_sorted_markdups_ARRG_recalibrated.bam -O Sample_aligned_sorted_markdups_ARRG_recalibrated.gvcf.gz -ERC GVCF
Using GATK jar /home/administrator/IGIB/gatk-4.1.4.0/gatk-package-4.1.4.0-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 -jar /home/administrator/IGIB/gatk-4.1.4.0/gatk-package-4.1.4.0-local.jar HaplotypeCaller -R /home/administrator/IGIB/samples/Homo_sapiens_assembly38.fasta -I Sample_aligned_sorted_markdups_ARRG_recalibrated.bam -O Sample_aligned_sorted_markdups_ARRG_recalibrated.gvcf.gz -ERC GVCF
03:33:11.585 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/administrator/IGIB/gatk-4.1.4.0/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
administrator@uarch-compression:~/IGIB/samples/for_intel$ numactl -N 0 -m 0 /home/administrator/IGIB/gatk-4.1.4.0/gatk --java-options "-Xmx50g" HaplotypeCaller -R "/home/administrator/IGIB/samples/Homo_sapiens_assembly38.fasta" -I Sample_aligned_sorted_markdups_ARRG_recalibrated.bam -O Sample_aligned_sorted_markdups_ARRG_recalibrated.gvcf.gz -ERC GVCF
Using GATK jar /home/administrator/IGIB/gatk-4.1.4.0/gatk-package-4.1.4.0-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 -jar /home/administrator/IGIB/gatk-4.1.4.0/gatk-package-4.1.4.0-local.jar HaplotypeCaller -R /home/administrator/IGIB/samples/Homo_sapiens_assembly38.fasta -I Sample_aligned_sorted_markdups_ARRG_recalibrated.bam -O Sample_aligned_sorted_markdups_ARRG_recalibrated.gvcf.gz -ERC GVCF
03:33:17.979 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/administrator/IGIB/gatk-4.1.4.0/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Nov 27, 2019 3:33:23 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
03:33:23.137 INFO HaplotypeCaller - ------------------------------------------------------------
03:33:23.138 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.4.0
03:33:23.138 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
03:33:23.138 INFO HaplotypeCaller - Executing as administrator@uarch-compression on Linux v4.4.0-142-generic amd64
03:33:23.138 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v9-internal+0-2016-04-14-195246.buildd.src
03:33:23.138 INFO HaplotypeCaller - Start Date/Time: 27 November 2019 at 3:33:17 AM IST
03:33:23.138 INFO HaplotypeCaller - ------------------------------------------------------------
03:33:23.138 INFO HaplotypeCaller - ------------------------------------------------------------
03:33:23.139 INFO HaplotypeCaller - HTSJDK Version: 2.20.3
03:33:23.139 INFO HaplotypeCaller - Picard Version: 2.21.1
03:33:23.139 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
03:33:23.139 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
03:33:23.139 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
03:33:23.139 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
03:33:23.139 INFO HaplotypeCaller - Deflater: IntelDeflater
03:33:23.139 INFO HaplotypeCaller - Inflater: IntelInflater
03:33:23.139 INFO HaplotypeCaller - GCS max retries/reopens: 20
03:33:23.139 INFO HaplotypeCaller - Requester pays: disabled
03:33:23.139 INFO HaplotypeCaller - Initializing engine
03:33:23.582 INFO HaplotypeCaller - Done initializing engine
03:33:23.584 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled
03:33:23.635 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
03:33:23.635 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output
03:33:23.646 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/administrator/IGIB/gatk-4.1.4.0/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
03:33:23.647 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/administrator/IGIB/gatk-4.1.4.0/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
03:33:23.694 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
03:33:23.694 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
03:33:23.695 INFO IntelPairHmm - Available threads: 52
03:33:23.695 INFO IntelPairHmm - Requested threads: 4
03:33:23.695 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
03:33:23.748 INFO ProgressMeter - Starting traversal
03:33:23.748 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
03:33:24.190 WARN InbreedingCoeff - InbreedingCoeff will not be calculated; at least 10 samples must have called genotypes
03:33:24.430 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 2.2298200000000001E-4
03:33:24.431 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.005144221
03:33:24.431 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.01 sec
03:33:24.431 INFO HaplotypeCaller - Shutting down engine
[27 November 2019 at 3:33:24 AM IST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=6442450944
java.lang.NullPointerException
at org.broadinstitute.hellbender.utils.read.AlignmentUtils.needsConsolidation(AlignmentUtils.java:758)
at org.broadinstitute.hellbender.utils.read.AlignmentUtils.consolidateCigar(AlignmentUtils.java:719)
at org.broadinstitute.hellbender.utils.read.AlignmentUtils.applyCigarToCigar(AlignmentUtils.java:1290)
at org.broadinstitute.hellbender.utils.read.AlignmentUtils.createReadAlignedToRef(AlignmentUtils.java:100)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils.realignReadsToTheirBestHaplotype(AssemblyBasedCallerUtils.java:85)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:606)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:240)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:308)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:281)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
I can not see an error.... what's the issue? Can you properly format the output of the log?
the error is here:
this is a problem in gatk. You should report it to https://github.com/broadinstitute/gatk/issues
Thanks for pointing that out. I missed it.
dishasharma should checkout this similarily asked question on the gatk forums: https://gatkforums.broadinstitute.org/gatk/discussion/13717/java-lang-nullpointerexception-in-haplotypecaller-when-generating-gvcf-with-gatk-4-0-11-0
I don't suggest creating an issue, but probably taking this question over to the gatk forum is a better solution.