The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

GATK -L option problem

HyunminHyunmin Seoul, KoreaMember
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...)

Best Answers

Answers

  • HyunminHyunmin Seoul, KoreaMember

    Thanks, via comment. I solve it.

Sign In or Register to comment.