reference error wile running CoverageBySample

markmark Member
edited October 2012 in Ask the GATK team

With the following command line:
java -jar GenomeAnalysisTKLite.jar -T CoverageBySample -I NGS0237-0014L_S5.ref_21563.bam -R 21563.fa -L 21563 -o out

I get

INFO 11:37:18,112 HelpFormatter - ---------------------------------------------------------------------------------
INFO 11:37:18,113 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-13-g0f021e6, Compiled 2012/10/12 17:51:55
INFO 11:37:18,113 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:37:18,113 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:37:18,114 HelpFormatter - Program Args: -T CoverageBySample -I NGS0237-0014L_S5.ref_21563.bam -R 21563.fa -L 21563 -o out
INFO 11:37:18,114 HelpFormatter - Date/Time: 2012/10/24 11:37:18
INFO 11:37:18,114 HelpFormatter - ---------------------------------------------------------------------------------
INFO 11:37:18,114 HelpFormatter - ---------------------------------------------------------------------------------
INFO 11:37:18,117 GenomeAnalysisEngine - Strictness is SILENT

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.1-13-g0f021e6):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Invalid command line: Failed to load reference dictionary
ERROR ------------------------------------------------------------------------------------------

My reference sequence is a fasta file as I believe is specified in the documentation and has no non-standard bases.

What's wrong?

Thanks for your help (I'm new to using GATK)

Mark

Answers

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