Help!Error: the contig index is greater then the stored sequence count

[HongxiangZheng]

Hi all

I have encountered the same problem as this http://seqanswers.com/forums/showthread.php?t=6937

Fowllowing the instruction on Local realignment around indels, I was able to go though the first step. However, the second step has some errors.
In additon, my GATK is the latest one. And, I dealed with mitochondrial genome, size of which is rather small for only 20+M.

Can anybody give some advice?

Here is the log:
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.sting.utils.exceptions.Reviewed StingException: Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count
at org.broadinstitute.sting.utils.GenomeLocParser.exc eptionOnInvalidGenomeLoc(GenomeLocParser.java:443)
at org.broadinstitute.sting.utils.GenomeLocParser.cre ateGenomeLoc(GenomeLocParser.java:403)
at org.broadinstitute.sting.gatk.iterators.VerifyingS amIterator.isOutOfOrder(VerifyingSamIterator.java: 51)
at org.broadinstitute.sting.gatk.iterators.VerifyingS amIterator.verifyRecord(VerifyingSamIterator.java: 41)
at org.broadinstitute.sting.gatk.iterators.VerifyingS amIterator.next(VerifyingSamIterator.java:34)
at org.broadinstitute.sting.gatk.iterators.VerifyingS amIterator.next(VerifyingSamIterator.java:18)
at org.broadinstitute.sting.gatk.filters.CountingFilt eringIterator.getNextRecord(CountingFilteringItera tor.java:106)
at org.broadinstitute.sting.gatk.filters.CountingFilt eringIterator.next(CountingFilteringIterator.java: 82)
at org.broadinstitute.sting.gatk.filters.CountingFilt eringIterator.next(CountingFilteringIterator.java: 42)
at org.broadinstitute.sting.gatk.iterators.PrivateStr ingSAMCloseableIterator.next(StingSAMIteratorAdapt er.java:100)
at org.broadinstitute.sting.gatk.iterators.PrivateStr ingSAMCloseableIterator.next(StingSAMIteratorAdapt er.java:84)
at org.broadinstitute.sting.gatk.datasources.simpleDa taSources.SAMDataSource.fillShard(SAMDataSource.ja va:375)
at org.broadinstitute.sting.gatk.datasources.shards.R eadShardStrategy.advance(ReadShardStrategy.java:15 4)
at org.broadinstitute.sting.gatk.datasources.shards.R eadShardStrategy.<init>(ReadShardStrategy.java:100 )
at org.broadinstitute.sting.gatk.datasources.shards.S hardStrategyFactory.shatter(ShardStrategyFactory.j ava:73)
at org.broadinstitute.sting.gatk.datasources.shards.S hardStrategyFactory.shatter(ShardStrategyFactory.j ava:55)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine .getShardStrategy(GenomeAnalysisEngine.java:333)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine .execute(GenomeAnalysisEngine.java:100)
at org.broadinstitute.sting.gatk.CommandLineExecutabl e.execute(CommandLineExecutable.java:97)
at org.broadinstitute.sting.commandline.CommandLinePr ogram.start(CommandLineProgram.java:244)
at org.broadinstitute.sting.gatk.CommandLineGATK.main (CommandLineGATK.java:87)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.4705):
##### ERROR
##### ERROR Please visit to wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### 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: Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count
##### ERROR ------------------------------------------------------------------------------------------

[HongxiangZheng]

Hi, the problem was solved by just download the offical reference sequences.
Thanks all.

[shirley_45060525]

Hi, the problem was solved by just download the offical reference sequences.
Thanks all.

I have download the offical reference sequences.
but the erro still appear in chrX and chrY.~~

[shirley_45060525]

My problem also was solved .You must be use the same reference in the aligned and GATK
~~