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GATK -L option problem

HyunminHyunmin Seoul, KoreaMember
edited August 2013 in Ask the GATK team

root@GR0001:~# java -Xmx2g -jar /nG/Process/Tools/GATK/GenomeAnalysisTK-2.7-1-g42d771f/GenomeAnalysisTK.jar -T RealignerTargetCreator -nt 3 -L 9 -R '/nG/Reference/CommonName/dog/FASTA/chrAll.fa' -I '/nG/Data/1265/vcf1/node1/9/Databind/9.bam' -o '/nG/Data/1265/vcf1/node1/9/Databind/9.bam.intervals'
INFO 11:10:17,730 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:10:17,732 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/21 23:02:55
INFO 11:10:17,733 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:10:17,733 HelpFormatter - For support and documentation go to
INFO 11:10:17,737 HelpFormatter - Program Args: -T RealignerTargetCreator -nt 3 -L 9 -R /nG/Reference/CommonName/dog/FASTA/chrAll.fa -I /nG/Data/1265/vcf1/node1/9/Databind/9.bam -o /nG/Data/1265/vcf1/node1/9/Databind/9.bam.intervals
INFO 11:10:17,738 HelpFormatter - Date/Time: 2013/08/28 11:10:17
INFO 11:10:17,738 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:10:17,738 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:10:17,879 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:10:18,189 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 11:10:18,198 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:10:18,325 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
INFO 11:10:24,257 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.7-1-g42d771f):
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 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 Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: Couldn't read file /root/9 because The interval file 9 does not have one of the supported extensions (.bed, .list, .picard, .interval_list, or .intervals). Please rename your file with the appropriate extension. If 9 is NOT supposed to be a file, please move or rename the file at location /root/9
ERROR ------------------------------------------------------------------------------------------

I can't understand why call this error.
please check it. Is it a bug?

When I try to with chromosome 9 (numerical), I have the problem. There is not problem for other chromosome number (like 1,2,3,4,5,6,7,8,10,11...)

Best Answers


  • HyunminHyunmin Seoul, KoreaMember

    Thanks, via comment. I solve it.

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