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Getting null point exception when running BaseRecalibrator

Hi all, I am running this command in

java -jar gatk-package.jar BaseRecalibrator -R RefGenomes/Felis_catus_new8.fna -I DS05061.bam -O DS05061.table --known-sites RefGenomes/felis_catus.vcf

and am getting this error:
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
04:34:40.657 INFO NativeLibraryLoader - Loading from jar:file:/home/users/cawthamy/gatk-package.jar!/com/intel/gkl/native/
04:34:46.444 INFO BaseRecalibrator - ------------------------------------------------------------
04:34:46.445 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.0.3.0
04:34:46.445 INFO BaseRecalibrator - For support and documentation go to
04:34:46.446 INFO BaseRecalibrator - Executing as [email protected] on Linux v3.10.0-693.11.6.el7.x86_64 amd64
04:34:46.446 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_151-b12
04:34:46.446 INFO BaseRecalibrator - Start Date/Time: May 30, 2018 4:34:40 AM EDT
04:34:46.446 INFO BaseRecalibrator - ------------------------------------------------------------
04:34:46.446 INFO BaseRecalibrator - ------------------------------------------------------------
04:34:46.447 INFO BaseRecalibrator - HTSJDK Version: 2.14.3
04:34:46.447 INFO BaseRecalibrator - Picard Version: 2.17.2
04:34:46.447 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
04:34:46.448 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
04:34:46.448 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
04:34:46.448 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
04:34:46.448 INFO BaseRecalibrator - Deflater: IntelDeflater
04:34:46.448 INFO BaseRecalibrator - Inflater: IntelInflater
04:34:46.448 INFO BaseRecalibrator - GCS max retries/reopens: 20
04:34:46.448 INFO BaseRecalibrator - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from
04:34:46.448 INFO BaseRecalibrator - Initializing engine
04:34:53.427 INFO FeatureManager - Using codec VCFCodec to read file file:///home/users/cawthamy/RefGenomes/felis_catus.vcf
04:34:53.450 INFO BaseRecalibrator - Shutting down engine
[May 30, 2018 4:34:53 AM EDT] done. Elapsed time: 0.21 minutes.
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getContigNames(
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getCommonContigsByName(
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.compareDictionaries(
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(
at org.broadinstitute.hellbender.engine.GATKTool.validateSequenceDictionaries(
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(
at org.broadinstitute.hellbender.engine.ReadWalker.onStartup(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(
at org.broadinstitute.hellbender.Main.runCommandLineProgram(
at org.broadinstitute.hellbender.Main.mainEntry(
at org.broadinstitute.hellbender.Main.main(

how can I fix this?

Best Answer


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