Question: gatk haplotypecaller crashing
0
gravatar for dishasharma35
6 months ago by
dishasharma350 wrote:

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)
sequencing dna java gatk • 388 views
ADD COMMENTlink modified 6 months ago by Pierre Lindenbaum128k • written 6 months ago by dishasharma350

I can not see an error.... what's the issue? Can you properly format the output of the log?

ADD REPLYlink written 6 months ago by Amar650

the error is here:

java.lang.NullPointerException
    at org.broadinstitute.hellbender.utils.read.AlignmentUtils.needsConsolidation(AlignmentUtils.java:758)

this is a problem in gatk. You should report it to https://github.com/broadinstitute/gatk/issues

ADD REPLYlink written 6 months ago by Pierre Lindenbaum128k

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.

ADD REPLYlink written 6 months ago by Amar650
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