GATK -L option problem

HyunminHyunmin Posts: 11Member
edited August 2013 in Ask the GATK team

root@GR0001:~# java -Xmx2g -Djava.io.tmpdir=/nG/Data/1265/vcf1/node1/9/AnalysisTemp/ -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 http://www.broadinstitute.org/gatk 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
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: 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?

update 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...)

Post edited by Hyunmin on

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  • HyunminHyunmin Posts: 11Member
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