Parameters to GenomeLocParser are incorrect ..... How to fix this in "SplitNCigarReads" version3.2

AbhisheknlAbhisheknl NetherlandsMember
edited August 2014 in Ask the GATK team

Hi,

I am using RNA-seq data for variant calling. I am stuck at the step of "SplitNCigarReads".

The command that, I am using is:

java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R hg19.fa -I Mydata.sort.MarkDup.RG.bam -o Mydata.sort.MarkDup.RG.split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS

Now, the error that I get is:

INFO  13:52:00,688 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  13:52:00,693 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 
INFO  13:52:00,694 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  13:52:00,694 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  13:52:00,705 HelpFormatter - Program Args: -T SplitNCigarReads -R hg19.fa -I Mydata.sort.MarkDup.RG.bam -o Mydata.sort.MarkDup.RG.split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS 
INFO  13:52:00,716 HelpFormatter - Executing as [email protected] on Linux 3.12.21-gentoo-r1 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_55-b13. 
INFO  13:52:00,719 HelpFormatter - Date/Time: 2014/08/28 13:52:00 
INFO  13:52:00,723 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  13:52:00,726 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  13:52:03,508 GenomeAnalysisEngine - Strictness is SILENT 
INFO  13:52:03,794 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  13:52:03,817 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  13:52:03,988 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.16 
INFO  13:52:04,627 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  13:52:04,666 GenomeAnalysisEngine - Done preparing for traversal 
INFO  13:52:04,672 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  13:52:04,678 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  13:52:04,683 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime 
INFO  13:52:05,021 ReadShardBalancer$1 - Loading BAM index data 
INFO  13:52:05,032 ReadShardBalancer$1 - Done loading BAM index data 
INFO  13:52:16,601 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.2-2-gec30cee): 
##### 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: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 0 is less than start 4 in contig chrM
##### ERROR ------------------------------------------------------------------------------------------

Kindly help in fixing this error.

Thank you

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