java -jar gatk -T IndelGenotyperV2 -l INFO -bed brief.bed -R /data/results/genomes/hg18/hg18.fa -I fastq.sorted.realigned.bam -o fastq_indel.txt -verbose fastq_indel_statistics.txt
This produces an error
"GenomeLocParser are incorrect:The stop position 1 is less than start 141481674"
does anyone know how to solve?
INFO 20:34:49,281 HelpFormatter - ---------------------------------------------------------------------------
INFO 20:34:49,283 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5974, Compiled 2011/06/10 13:26:59
INFO 20:34:49,283 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 20:34:49,283 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 20:34:49,283 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 20:34:49,284 HelpFormatter - Program Args: -T IndelGenotyperV2 -l INFO -bed brief.bed -R /data/results/genomes/hg18/hg18.fa -I fastq.sorted.realigned.bam -o fastq_indel.txt -verbose fastq_indel_statistics.txt
INFO 20:34:49,284 HelpFormatter - Date/Time: 2011/06/16 20:34:49
INFO 20:34:49,284 HelpFormatter - ---------------------------------------------------------------------------
INFO 20:34:49,284 HelpFormatter - ---------------------------------------------------------------------------
INFO 20:34:49,295 GenomeAnalysisEngine - Strictness is SILENT
INFO 20:36:05,521 IndelGenotyperV2Walker - No gene annotations available
INFO 20:37:25,387 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
INFO 20:37:25,388 TraversalEngine - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 20:37:25,392 TraversalEngine - chr1:18958321 1.00e+00 79.9 s 132.1 w 0.6% 3.6 h 3.6 h
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.0.5974):
##### 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 stop position 1 is less than start 141481674
##### ERROR ------------------------------------------------------------------------------------------
This produces an error
"GenomeLocParser are incorrect:The stop position 1 is less than start 141481674"
does anyone know how to solve?
INFO 20:34:49,281 HelpFormatter - ---------------------------------------------------------------------------
INFO 20:34:49,283 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5974, Compiled 2011/06/10 13:26:59
INFO 20:34:49,283 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 20:34:49,283 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 20:34:49,283 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 20:34:49,284 HelpFormatter - Program Args: -T IndelGenotyperV2 -l INFO -bed brief.bed -R /data/results/genomes/hg18/hg18.fa -I fastq.sorted.realigned.bam -o fastq_indel.txt -verbose fastq_indel_statistics.txt
INFO 20:34:49,284 HelpFormatter - Date/Time: 2011/06/16 20:34:49
INFO 20:34:49,284 HelpFormatter - ---------------------------------------------------------------------------
INFO 20:34:49,284 HelpFormatter - ---------------------------------------------------------------------------
INFO 20:34:49,295 GenomeAnalysisEngine - Strictness is SILENT
INFO 20:36:05,521 IndelGenotyperV2Walker - No gene annotations available
INFO 20:37:25,387 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
INFO 20:37:25,388 TraversalEngine - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 20:37:25,392 TraversalEngine - chr1:18958321 1.00e+00 79.9 s 132.1 w 0.6% 3.6 h 3.6 h
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.0.5974):
##### 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 stop position 1 is less than start 141481674
##### ERROR ------------------------------------------------------------------------------------------
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