Hi,
I am trying to run CNNScoreVariants on an exome using:
java -jar $GATK CNNScoreVariants -V ERR000589.raw.vcf -R $REFERENCE -O ERR000589.CNN.vcf
I have a bam file, aligned with BWA with read headers with a local version of GATK4 (4.1.2.0).
The tool seems to run to completion but fails to produce a vcf file after scoring.
12:50:54.774 INFO CNNScoreVariants - ------------------------------------------------------------
12:50:54.774 INFO CNNScoreVariants - The Genome Analysis Toolkit (GATK) v4.1.2.0
12:50:54.774 INFO CNNScoreVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
12:50:54.774 INFO CNNScoreVariants - Executing as ricardo@ricardo-G750JW on Linux v4.15.0-50-generic amd64
12:50:54.774 INFO CNNScoreVariants - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.18.04.1-b03
12:50:54.775 INFO CNNScoreVariants - Start Date/Time: May 24, 2019 12:50:52 EDT PM
12:50:54.775 INFO CNNScoreVariants - ------------------------------------------------------------
12:50:54.775 INFO CNNScoreVariants - ------------------------------------------------------------
12:50:54.775 INFO CNNScoreVariants - HTSJDK Version: 2.19.0
12:50:54.775 INFO CNNScoreVariants - Picard Version: 2.19.0
12:50:54.775 INFO CNNScoreVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:50:54.775 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:50:54.775 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:50:54.775 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:50:54.775 INFO CNNScoreVariants - Deflater: IntelDeflater
12:50:54.776 INFO CNNScoreVariants - Inflater: IntelInflater
12:50:54.776 INFO CNNScoreVariants - GCS max retries/reopens: 20
12:50:54.776 INFO CNNScoreVariants - Requester pays: disabled
12:50:54.776 INFO CNNScoreVariants - Initializing engine
12:50:55.024 INFO FeatureManager - Using codec VCFCodec to read file file:///home/ricardo/Downloads/gatk-4.1.1.0/wdl/ERR000589.raw.vcf
12:50:55.081 INFO CNNScoreVariants - Done initializing engine
12:50:55.082 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/ricardo/Downloads/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
12:50:55.147 INFO CNNScoreVariants - Done scoring variants with CNN.
12:50:55.147 INFO CNNScoreVariants - Shutting down engine
[May 24, 2019 12:50:55 EDT PM] org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=632815616
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:307)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1037)
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:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Thanks for you help,
Ricardo