Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • nvteja
    Junior Member
    • Jan 2010
    • 5
    #1

    GATK error

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


    To report bugs or to get help resolving undocumented issues, please contact us via our support site at:
    503 Service Temporarily Unavailable
    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.
    Tags: None
  • HongxiangZheng
    Junior Member
    • Dec 2010
    • 5
    #2
    Help!Error: the contig index is greater then the stored sequence count

    Originally posted by nvteja View Post
    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:
    Access Denied
    http://www.broadinstitute.org/gsa/wiki


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

    Comment

    Previous template Next

    Latest Articles

    Collapse
    • SEQadmin2
      Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
      by SEQadmin2



      Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
      ...
      07-09-2026, 11:10 AM
    • SEQadmin2
      Cancer Drug Resistance: The Lingering Barrier to Rising Survival
      by SEQadmin2



      Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

      There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
      07-08-2026, 05:17 AM
    • GATTACAT
      Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
      by GATTACAT
      Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
      07-01-2026, 11:43 AM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    UC San Diego Bioengineers Map Gene Function in Human Stem Cells by SEQadmin2
    Started by SEQadmin2, 07-13-2026, 10:26 AM
    0 responses
    24 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    07-13-2026, 10:26 AM  
    New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2
    Started by SEQadmin2, 07-09-2026, 10:04 AM
    0 responses
    34 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    07-09-2026, 10:04 AM  
    Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2
    Started by SEQadmin2, 07-08-2026, 10:08 AM
    0 responses
    21 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    07-08-2026, 10:08 AM  
    Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2
    Started by SEQadmin2, 07-07-2026, 11:05 AM
    0 responses
    34 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    07-07-2026, 11:05 AM  
    View All
    Working...