SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
[SNP calling, GATK] this contig isn't present in the Fasta sequence dictionar sehrrot Bioinformatics 3 05-30-2012 11:17 PM
GATK count covariates error - contig lengths Hkins552 Bioinformatics 0 07-05-2011 08:16 AM
SRMA Problem SAMRecord contig does not match the current reference sequence contig gavin.oliver Bioinformatics 5 07-05-2011 06:28 AM
Help!Error: the contig index is greater then the stored sequence count HongxiangZheng Bioinformatics 3 05-14-2011 02:35 AM

Reply
 
Thread Tools
Old 07-23-2012, 12:54 PM   #1
Lessthan3
Junior Member
 
Location: West Korea

Join Date: Jul 2012
Posts: 2
Default GATK::The contig index 20 is greater than the stored sequence count (1)

Beginner in bioinformatics,

So when I use the GATK command
Code:
java -jar GenomeAnalysisTK.jar -I MYBAM.bam -R MYFASTA.fa -T CountReads
I get the following error:
Code:
INFO  15:46:15,479 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:46:15,481 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56 .orgftp://gsapubftp-anonymous@ftp.broadinsti
INFO  15:46:15,481 HelpFormatter - Copyright (c) 2010 The Broad Institute bam -R chr21.fa -T CountReads
INFO  15:46:15,481 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki 
INFO  15:46:15,481 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa 
INFO  15:46:15,482 HelpFormatter - Program Args: -I sorted_indexed.bam -R chr21.fa -T CountReads 
INFO  15:46:15,482 HelpFormatter - Date/Time: 2012/07/23 15:46:15 
INFO  15:46:15,483 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:46:15,483 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:46:15,487 GenomeAnalysisEngine - Strictness is SILENT 
INFO  15:46:15,526 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  15:46:15,546 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 
INFO  15:46:16,278 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.6-13-g91f02df): 
##### 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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The contig index 20 is greater than the stored sequence count (1)
##### ERROR ------------------------------------------------------------------------------------------
I sorted MYBAM, added read groups, and indexed it.
The MYBAM corresponds to chromosome 21, and I got MYFASTA from http://hgdownload.cse.ucsc.edu/golde...8/chromosomes/ for chr21.

Please help solve this.

Thanks!
Lessthan3 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:55 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO