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gatk4 FilterMutectCalls Error

Hi I have run gatk4 mutect2 for tumor only samples using WGS data and was trying to filter them using FIlterMutectCalls but got some error:

-rw-rw---- 1 xxx xxx 195313532 Aug 17 09:15 S9-MuTect2-GATK4.0.1.1.vcf.gz
-rw-rw---- 1 xxx xxx 10897979 Aug 17 09:15 S9-MuTect2-GATK4.0.1.1.vcf.idx

$ java -jar /opt/NGS/GATK/gatk- FilterMutectCalls -V S9-MuTect2-GATK4.0.1.1.vcf.gz -O test.vcf.gz
09:21:46.624 INFO NativeLibraryLoader - Loading from jar:file:/opt/NGS/GATK/gatk-!/com/intel/gkl/native/
09:21:46.728 INFO FilterMutectCalls - ------------------------------------------------------------
09:21:46.728 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.0.1.1
09:21:46.728 INFO FilterMutectCalls - For support and documentation go to
09:21:46.729 INFO FilterMutectCalls - Executing as [email protected] on Linux v4.15.0-24-generic amd64
09:21:46.729 INFO FilterMutectCalls - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_172-b11
09:21:46.729 INFO FilterMutectCalls - Start Date/Time: August 17, 2018 9:21:46 AM EDT
09:21:46.729 INFO FilterMutectCalls - ------------------------------------------------------------
09:21:46.729 INFO FilterMutectCalls - ------------------------------------------------------------
09:21:46.730 INFO FilterMutectCalls - HTSJDK Version: 2.14.1
09:21:46.730 INFO FilterMutectCalls - Picard Version: 2.17.2
09:21:46.730 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 1
09:21:46.730 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:21:46.730 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:21:46.730 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:21:46.730 INFO FilterMutectCalls - Deflater: IntelDeflater
09:21:46.730 INFO FilterMutectCalls - Inflater: IntelInflater
09:21:46.730 INFO FilterMutectCalls - GCS max retries/reopens: 20
09:21:46.730 INFO FilterMutectCalls - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from
09:21:46.730 INFO FilterMutectCalls - Initializing engine
09:21:49.393 INFO FilterMutectCalls - Shutting down engine
[August 17, 2018 9:21:49 AM EDT] done. Elapsed time: 0.05 minutes.

A USER ERROR has occurred: Cannot read S9-MuTect2-GATK4.0.1.1.vcf.gz because no suitable codecs found

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Best Answer


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