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Error while running BaseRecalibrator

java -jar Tools/GenomeAnalysisTK.jar -T PrintReads -R Reference/BWA/Homo_sapiens_assembly38.fasta -I output/sample1/BWA_alignment_RG.bam -BQSR output/sample1/BWA_alignment_recall_data.table -o output/sample1/BWA_recal.bam
INFO 09:14:21,764 HelpFormatter - ---------------------------------------------------------------------------------
INFO 09:14:21,766 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
INFO 09:14:21,766 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 09:14:21,766 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 09:14:21,769 HelpFormatter - Program Args: -T PrintReads -R Reference/BWA/Homo_sapiens_assembly38.fasta -I output/sample1/BWA_alignment_RG.bam -BQSR output/sample1/BWA_alignment_recall_data.table -o output/sample1/BWA_recal.bam
INFO 09:14:21,771 HelpFormatter - Executing as bioinformatics@BIF-Server on Linux 3.19.0-56-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_77-b03.
INFO 09:14:21,772 HelpFormatter - Date/Time: 2016/04/13 09:14:21
INFO 09:14:21,772 HelpFormatter - ---------------------------------------------------------------------------------
INFO 09:14:21,772 HelpFormatter - ---------------------------------------------------------------------------------
INFO 09:14:22,267 GenomeAnalysisEngine - Strictness is SILENT

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.4-46-gbc02625):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Bad input: The GATK report has no version specified in the header
ERROR ------------------------------------------------------------------------------------------

Issue · Github
by Sheila

Issue Number
817
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

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