CNNScoreVariants carshes with java.lang.NullPointerException with Python 3.8 & JDK 1.8
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.4.1
b) Exact command used:
gatk CNNScoreVariants -VVCF_FILE.vcf -R CHAR.Chr.fa -O output.vcf
c) Entire error log:
14:23:50.557 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/GATK/4.1.4.1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Oct 08, 2021 2:23:50 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
14:23:50.859 INFO CNNScoreVariants - ------------------------------------------------------------
14:23:50.860 INFO CNNScoreVariants - The Genome Analysis Toolkit (GATK) v4.1.4.1
14:23:50.860 INFO CNNScoreVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
14:23:50.860 INFO CNNScoreVariants - Executing as wzi_sur@srnode29 on Linux v3.10.0-1160.el7.x86_64 amd64
14:23:50.860 INFO CNNScoreVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_25-b17
14:23:50.860 INFO CNNScoreVariants - Start Date/Time: October 8, 2021 2:23:50 PM CEST
14:23:50.860 INFO CNNScoreVariants - ------------------------------------------------------------
14:23:50.860 INFO CNNScoreVariants - ------------------------------------------------------------
14:23:50.860 INFO CNNScoreVariants - HTSJDK Version: 2.21.0
14:23:50.860 INFO CNNScoreVariants - Picard Version: 2.21.2
14:23:50.860 INFO CNNScoreVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:23:50.860 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:23:50.861 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:23:50.861 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:23:50.861 INFO CNNScoreVariants - Deflater: IntelDeflater
14:23:50.861 INFO CNNScoreVariants - Inflater: IntelInflater
14:23:50.861 INFO CNNScoreVariants - GCS max retries/reopens: 20
14:23:50.861 INFO CNNScoreVariants - Requester pays: disabled
14:23:50.861 INFO CNNScoreVariants - Initializing engine
14:23:51.192 INFO FeatureManager - Using codec VCFCodec to read file file:///VCF_FILE.vcf
14:23:51.280 INFO CNNScoreVariants - Done initializing engine
14:23:51.281 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/GATK/4.1.4.1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
14:23:51.407 INFO CNNScoreVariants - Done scoring variants with CNN.
14:23:51.407 INFO CNNScoreVariants - Shutting down engine
[October 8, 2021 2:23:51 PM CEST] org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2271215616
java.lang.NullPointerException
at org.broadinstitute.hellbender.utils.runtime.ProcessControllerAckResult.hasMessage(ProcessControllerAckResult.java:49)
at org.broadinstitute.hellbender.utils.runtime.ProcessControllerAckResult.getDisplayMessage(ProcessControllerAckResult.java:69)
at org.broadinstitute.hellbender.utils.runtime.StreamingProcessController.waitForAck(StreamingProcessController.java:229)
at org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor.waitForAck(StreamingPythonScriptExecutor.java:216)
at org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor.sendSynchronousCommand(StreamingPythonScriptExecutor.java:183)
at org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.onTraversalStart(CNNScoreVariants.java:317)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1046)
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)
Using GATK jar /GATK/4.1.4.1/gatk-package-4.1.4.1-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 /GATK/4.1.4.1/gatk-package-4.1.4.1-local.jar CNNScoreVariants -V VCF_FILE.vcf -R CHAR.Chr.fa -O output.vcf
-
Could you take a look at this previous forum post of the same issue and let me know if the suggestions in it are helpful? I would also recommend upgrading to a newer version of GATK as there have been significant improvements and bug fixes since the version you are using.
Kind regards,
Pamela
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