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  • A GATK RUNTIME ERROR has occurred

    I am new to GATK. Today, I run
    Code:
    java -jar /media/zwang10/Elements/UK10K/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T CountLoci -R /media/zwang10/Elements/UK10K/human_g1k_v37.fasta -I _EGAR00001038931_36843.pe.raw.sorted.bam
    But I got
    Code:
    INFO  14:59:39,061 HelpFormatter - -------------------------------------------------------------------------------- 
    INFO  14:59:39,064 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56 
    INFO  14:59:39,064 HelpFormatter - Copyright (c) 2010 The Broad Institute 
    INFO  14:59:39,064 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
    INFO  14:59:39,068 HelpFormatter - Program Args: -T CountReads -R /media/zwang10/Elements/UK10K/human_g1k_v37.fasta -I _EGAR00001038931_36843.pe.raw.sorted.bam 
    INFO  14:59:39,076 HelpFormatter - Executing as zwang10@office on Linux 3.13.0-74-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b02. 
    INFO  14:59:39,077 HelpFormatter - Date/Time: 2016/01/03 14:59:39 
    INFO  14:59:39,077 HelpFormatter - -------------------------------------------------------------------------------- 
    INFO  14:59:39,077 HelpFormatter - -------------------------------------------------------------------------------- 
    INFO  14:59:39,138 GenomeAnalysisEngine - Strictness is SILENT 
    INFO  14:59:39,342 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
    INFO  14:59:39,354 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
    INFO  14:59:39,416 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06 
    INFO  14:59:42,897 GATKRunReport - Uploaded run statistics report to AWS S3 
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace 
    org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to open index file (mark/reset not supported)_EGAR00001038931_36843.pe.raw.sorted.bam.bai
    	at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.openIndexFile(GATKBAMIndex.java:319)
    	at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.<init>(GATKBAMIndex.java:97)
    	at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.<init>(SAMDataSource.java:388)
    	at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.createReadsDataSource(GenomeAnalysisEngine.java:931)
    	at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:822)
    	at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
    	at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    	at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    	at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    	at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
    Caused by: java.io.IOException: mark/reset not supported
    	at java.io.InputStream.reset(InputStream.java:347)
    	at htsjdk.samtools.SamIndexes.asBaiSeekableStreamOrNull(SamIndexes.java:80)
    	at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.openIndexFile(GATKBAMIndex.java:314)
    	... 9 more
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
    ##### ERROR
    ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
    ##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
    ##### ERROR Visit our website and forum for extensive documentation and answers to 
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR MESSAGE: Unable to open index file (mark/reset not supported)_EGAR00001038931_36843.pe.raw.sorted.bam.bai
    ##### ERROR ------------------------------------------------------------------------------------------
    zwang10@office:/media/zwang10/Elements/UK10K$ java -jar /media/zwang10/Elements/UK10K/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T CountReads -R /media/zwang10/Elements/UK10K/human_g1k_v37.fasta -I _EGAR00001038931_36843.pe.raw.sorted.bam > temp
    INFO  15:08:54,928 HelpFormatter - -------------------------------------------------------------------------------- 
    INFO  15:08:54,931 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56 
    INFO  15:08:54,931 HelpFormatter - Copyright (c) 2010 The Broad Institute 
    INFO  15:08:54,931 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
    INFO  15:08:54,935 HelpFormatter - Program Args: -T CountReads -R /media/zwang10/Elements/UK10K/human_g1k_v37.fasta -I _EGAR00001038931_36843.pe.raw.sorted.bam 
    INFO  15:08:54,943 HelpFormatter - Executing as zwang10@office on Linux 3.13.0-74-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b02. 
    INFO  15:08:54,943 HelpFormatter - Date/Time: 2016/01/03 15:08:54 
    INFO  15:08:54,943 HelpFormatter - -------------------------------------------------------------------------------- 
    INFO  15:08:54,944 HelpFormatter - -------------------------------------------------------------------------------- 
    INFO  15:08:55,005 GenomeAnalysisEngine - Strictness is SILENT 
    INFO  15:08:55,171 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
    INFO  15:08:55,181 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
    INFO  15:08:55,237 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06 
    INFO  15:08:57,411 GATKRunReport - Uploaded run statistics report to AWS S3 
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace 
    org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to open index file (mark/reset not supported)_EGAR00001038931_36843.pe.raw.sorted.bam.bai
    	at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.openIndexFile(GATKBAMIndex.java:319)
    	at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.<init>(GATKBAMIndex.java:97)
    	at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.<init>(SAMDataSource.java:388)
    	at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.createReadsDataSource(GenomeAnalysisEngine.java:931)
    	at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:822)
    	at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
    	at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    	at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    	at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    	at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
    Caused by: java.io.IOException: mark/reset not supported
    	at java.io.InputStream.reset(InputStream.java:347)
    	at htsjdk.samtools.SamIndexes.asBaiSeekableStreamOrNull(SamIndexes.java:80)
    	at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.openIndexFile(GATKBAMIndex.java:314)
    	... 9 more
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
    ##### ERROR
    ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
    ##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
    ##### ERROR Visit our website and forum for extensive documentation and answers to 
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR MESSAGE: Unable to open index file (mark/reset not supported)_EGAR00001038931_36843.pe.raw.sorted.bam.bai
    ##### ERROR ------------------------------------------------------------------------------------------
    I did check _EGAR00001038931_36843.pe.raw.sorted.bam.bai is in the same folder.
    What happened?

  • #2
    I have no idea, but I wouldn't start a filename with an underscore.

    Comment


    • #3
      Originally posted by blancha View Post
      I have no idea, but I wouldn't start a filename with an underscore.
      It is the original name of the file. Do I need to change it?

      Comment


      • #4
        Certainly worth trying.

        Remember to rename both bam and index files. Not sure if the file name is embedded in the index, otherwise you may need to re-index the bam after changing the name.

        Comment


        • #5
          Originally posted by GenoMax View Post
          Certainly worth trying.

          Remember to rename both bam and index files. Not sure if the file name is embedded in the index, otherwise you may need to re-index the bam after changing the name.
          I changed name as EGAR00001038931.36843.pe.raw.sorted.bam and EGAR00001038931.36843.pe.raw.sorted.bam.bai


          I still get the same problem.

          Comment

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