GATK error

[nvteja]

Hi all,

I am trying to use GATK indel realigner to realign indels on one of the bam files. I was able to get the interval file but in the second step when I use by bam file to realign the indels , GATK is throwing the following error after it has processed 60,000,000 reads .


The exact command that I have used is

/usr/java/jre1.6.0_21/bin/java -Xmx2g -Djava.io.tmpdir=/cchome/vnelakud/GenomeAnalysisTK-1.0.4168/ -jar GenomeAnalysisTK.jar -I /biodbB/DasLab/Teja/Solexa_files/Casey_results_for_test_sample/s_1.mdup.srt.bam -R /cchome/vnelakud/Reference/Full_genome_reference.fa -T IndelRealigner -targetIntervals realign.intervals --targetIntervalsAreNotSorted -o s_1_indel_realigned.bam

And the error message

FATAL 12:01:59,225 CommandLineProgram -

------------------------------------------------------------------------------------------
The following error has occurred:

org.broadinstitute.sting.utils.StingException: Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count:

Please check your command line arguments for any typos or inconsistencies.
Also, please review our documentation at:

http://www.broadinstitute.org/gsa/wiki

To report bugs or to get help resolving undocumented issues, please contact us via our support site at:

http://getsatisfaction.com/gsa

Please be sure to include the stack trace below when posting a message on the support site:
------------------------------------------------------------------------------------------
java.lang.RuntimeException: org.broadinstitute.sting.utils.StingException: Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:259)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)
Caused by: org.broadinstitute.sting.utils.StingException: Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count
at org.broadinstitute.sting.utils.GenomeLocParser.exceptionOnInvalidGenomeLoc(GenomeLocParser.java:515)
at org.broadinstitute.sting.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:455)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.isOutOfOrder(VerifyingSamIterator.java:58)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.verifyRecord(VerifyingSamIterator.java:47)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:32)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:18)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:106)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:82)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:42)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:103)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:87)
at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.fillShard(SAMDataSource.java:304)
at org.broadinstitute.sting.gatk.datasources.shards.ReadShardStrategy.advance(ReadShardStrategy.java:156)
at org.broadinstitute.sting.gatk.datasources.shards.ReadShardStrategy.next(ReadShardStrategy.java:120)
at org.broadinstitute.sting.gatk.datasources.shards.ReadShardStrategy.next(ReadShardStrategy.java:43)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:51)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:186)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:84)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
... 1 more


I did check the command that I typed, but there are no errors in that.


Thanks for the help,
Teja.

[HongxiangZheng]

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

Hi all,

I am trying to use GATK indel realigner to realign indels on one of the bam files. I was able to get the interval file but in the second step when I use by bam file to realign the indels , GATK is throwing the following error after it has processed 60,000,000 reads .


The exact command that I have used is

/usr/java/jre1.6.0_21/bin/java -Xmx2g -Djava.io.tmpdir=/cchome/vnelakud/GenomeAnalysisTK-1.0.4168/ -jar GenomeAnalysisTK.jar -I /biodbB/DasLab/Teja/Solexa_files/Casey_results_for_test_sample/s_1.mdup.srt.bam -R /cchome/vnelakud/Reference/Full_genome_reference.fa -T IndelRealigner -targetIntervals realign.intervals --targetIntervalsAreNotSorted -o s_1_indel_realigned.bam

And the error message

FATAL 12:01:59,225 CommandLineProgram -

------------------------------------------------------------------------------------------
The following error has occurred:

org.broadinstitute.sting.utils.StingException: Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count:

Please check your command line arguments for any typos or inconsistencies.
Also, please review our documentation at:

http://www.broadinstitute.org/gsa/wiki

To report bugs or to get help resolving undocumented issues, please contact us via our support site at:

http://getsatisfaction.com/gsa

Please be sure to include the stack trace below when posting a message on the support site:
------------------------------------------------------------------------------------------
java.lang.RuntimeException: org.broadinstitute.sting.utils.StingException: Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:259)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)
Caused by: org.broadinstitute.sting.utils.StingException: Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count
at org.broadinstitute.sting.utils.GenomeLocParser.exceptionOnInvalidGenomeLoc(GenomeLocParser.java:515)
at org.broadinstitute.sting.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:455)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.isOutOfOrder(VerifyingSamIterator.java:58)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.verifyRecord(VerifyingSamIterator.java:47)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:32)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:18)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:106)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:82)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:42)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:103)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:87)
at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.fillShard(SAMDataSource.java:304)
at org.broadinstitute.sting.gatk.datasources.shards.ReadShardStrategy.advance(ReadShardStrategy.java:156)
at org.broadinstitute.sting.gatk.datasources.shards.ReadShardStrategy.next(ReadShardStrategy.java:120)
at org.broadinstitute.sting.gatk.datasources.shards.ReadShardStrategy.next(ReadShardStrategy.java:43)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:51)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:186)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:84)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
... 1 more


I did check the command that I typed, but there are no errors in that.


Thanks for the help,
Teja.

I have encountered the same problem above.
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.ReviewedStingException: Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count
at org.broadinstitute.sting.utils.GenomeLocParser.exceptionOnInvalidGenomeLoc(GenomeLocParser.java:443)
at org.broadinstitute.sting.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:403)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.isOutOfOrder(VerifyingSamIterator.java:51)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.verifyRecord(VerifyingSamIterator.java:41)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:34)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:18)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:106)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:82)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:42)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84)
at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.fillShard(SAMDataSource.java:375)
at org.broadinstitute.sting.gatk.datasources.shards.ReadShardStrategy.advance(ReadShardStrategy.java:154)
at org.broadinstitute.sting.gatk.datasources.shards.ReadShardStrategy.<init>(ReadShardStrategy.java:100)
at org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory.shatter(ShardStrategyFactory.java:73)
at org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory.shatter(ShardStrategyFactory.java: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.CommandLineExecutable.execute(CommandLineExecutable.java:97)
at org.broadinstitute.sting.commandline.CommandLineProgram.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 ------------------------------------------------------------------------------------------