"no suitable codecs found" by using CreateSomaticPanelOfNormals
a) GATK version I used: gatk-4.1.8.1
b) Exact command used: java -jar ~/tools/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar CreateSomaticPanelOfNormals -V normals_for_pon_vcf.args -O test.vcf.gz
c) Entire error log:
16:00:11.502 INFO CreateSomaticPanelOfNormals - ------------------------------------------------------------
16:00:11.502 INFO CreateSomaticPanelOfNormals - The Genome Analysis Toolkit (GATK) v4.1.8.1
16:00:11.503 INFO CreateSomaticPanelOfNormals - For support and documentation go to https://software.broadinstitute.org/gatk/
16:00:11.503 INFO CreateSomaticPanelOfNormals - Executing as user@x3650m4-2 on Linux v4.4.0-197-generic amd64
16:00:11.503 INFO CreateSomaticPanelOfNormals - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_275-8u275-b01-0ubuntu1~16.04-b01
16:00:11.503 INFO CreateSomaticPanelOfNormals - Start Date/Time: December 21, 2020 4:00:11 PM CST
16:00:11.503 INFO CreateSomaticPanelOfNormals - ------------------------------------------------------------
16:00:11.503 INFO CreateSomaticPanelOfNormals - ------------------------------------------------------------
16:00:11.504 INFO CreateSomaticPanelOfNormals - HTSJDK Version: 2.23.0
16:00:11.504 INFO CreateSomaticPanelOfNormals - Picard Version: 2.22.8
16:00:11.504 INFO CreateSomaticPanelOfNormals - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:00:11.504 INFO CreateSomaticPanelOfNormals - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:00:11.504 INFO CreateSomaticPanelOfNormals - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:00:11.504 INFO CreateSomaticPanelOfNormals - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:00:11.504 INFO CreateSomaticPanelOfNormals - Deflater: IntelDeflater
16:00:11.504 INFO CreateSomaticPanelOfNormals - Inflater: IntelInflater
16:00:11.504 INFO CreateSomaticPanelOfNormals - GCS max retries/reopens: 20
16:00:11.505 INFO CreateSomaticPanelOfNormals - Requester pays: disabled
16:00:11.505 WARN CreateSomaticPanelOfNormals -
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CreateSomaticPanelOfNormals is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
16:00:11.505 INFO CreateSomaticPanelOfNormals - Initializing engine
16:00:11.814 INFO CreateSomaticPanelOfNormals - Shutting down engine
[December 21, 2020 4:00:11 PM CST] org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1987575808
***********************************************************************
A USER ERROR has occurred: Cannot read file:///home/user/STR/test_bam/Lin/202012/Mutect2_output/normals_for_pon_vcf.args 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.
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Hi Hsu Pei-Chun, were you able to solve this issue? Your question was posted while our GATK Team was Out of Office and we did not get to your question.
If you still would like support from the GATK Team, please repost your question with [Repost] in the title and we will get to it as soon as possible.
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