Re: [svtoolkit-help] Invalid file pointer

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It is likely that your bam file or bam index file is corrupted.
I would try reindexing the file with "samtools index C046.bam"
If this doesn't fix the problem, I would try "samtools view" to see if 
samtools can read the file successfully.
-Bob

On 10/6/12 3:33 AM, yw wrote:
> Hi all,
> I used Genome-STRIP recently. I believe I have successfully installed
> the software. The install test was okay. And I tried with 30 BAM files
> and got the results. However, When I came to more BAM files, some of the
> BAM files went wrong. Here is the error message:
>
> java -Xmx4g
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/all_tmpdir
> -cp
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar
> org.broadinstitute.sting.gatk.CommandLineGATK -T
> ComputeInsertSizeHistograms -R
> /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I
> /home/wbxie/bam_file_MSUv7/C046.bam -O
> /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/metadata/isd/C046.hist.bin
> -md wild_rice_test2/metadata -createEmpty
> INFO 15:19:52,903 HelpFormatter -
> -----------------------------------------------------------------------------------
>
> INFO 15:19:52,908 HelpFormatter - The Genome Analysis Toolkit (GATK)
> v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29
> INFO 15:19:52,909 HelpFormatter - Copyright (c) 2010 The Broad Institute
> INFO 15:19:52,909 HelpFormatter - Please view our documentation at
> http://www.broadinstitute.org/gsa/wiki
> INFO 15:19:52,910 HelpFormatter - For support, please view our support
> site at http://getsatisfaction.com/gsa
> INFO 15:19:52,910 HelpFormatter - Program Args: -T
> ComputeInsertSizeHistograms -R
> /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I
> /home/wbxie/bam_file_MSUv7/C046.bam -O
> /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/metadata/isd/C046.hist.bin
> -md wild_rice_test2/metadata -createEmpty
> INFO 15:19:52,911 HelpFormatter - Date/Time: 2012/10/06 15:19:52
> INFO 15:19:52,911 HelpFormatter -
> -----------------------------------------------------------------------------------
>
> INFO 15:19:52,912 HelpFormatter -
> -----------------------------------------------------------------------------------
>
> INFO 15:19:52,922 GenomeAnalysisEngine - Strictness is SILENT
> INFO 15:19:54,579 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL
> STARTING]
> INFO 15:19:54,579 TraversalEngine - Location processed.reads runtime
> per.1M.reads completed total.runtime remaining
> INFO 15:20:04,247 TraversalEngine - chr01:24865802 1.24e+06 10.0 s 8.1 s
> 6.8% 2.5 m 2.3 m
> INFO 15:20:14,247 TraversalEngine - chr02:31101998 2.69e+06 20.0 s 7.4 s
> 20.0% 100.0 s 80.0 s
> INFO 15:20:24,291 TraversalEngine - chr04:9103726 4.11e+06 30.0 s 7.3 s
> 33.4% 89.9 s 59.9 s
> INFO 15:20:34,292 TraversalEngine - chr05:15404145 5.53e+06 40.0 s 7.2 s
> 44.6% 89.9 s 49.8 s
> INFO 15:20:44,293 TraversalEngine - chr07:4981864 6.98e+06 50.1 s 7.2 s
> 58.1% 86.1 s 36.1 s
> INFO 15:20:54,303 TraversalEngine - chr08:24859331 8.42e+06 60.1 s 7.1 s
> 71.3% 84.2 s 24.2 s
> INFO 15:21:04,347 TraversalEngine - chr10:12704502 9.76e+06 70.1 s 7.2 s
> 81.8% 85.7 s 15.6 s
> INFO 15:21:14,387 TraversalEngine - chr12:14627327 1.12e+07 80.1 s 7.1 s
> 96.2% 83.3 s 3.1 s
> ##### ERROR
> ------------------------------------------------------------------------------------------
> ##### ERROR stack trace
> java.lang.RuntimeException: Invalid file pointer: 71767958683648
> at
> net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:477)
> at
> net.sf.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:577)
> at net.sf.samtools.BAMFileReader.getIterator(BAMFileReader.java:243)
> at net.sf.samtools.SAMFileReader.iterator(SAMFileReader.java:314)
> at
> org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.getIterator(SAMDataSource.java:557)
> at
> org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.fillShard(SAMDataSource.java:482)
> at
> org.broadinstitute.sting.gatk.datasources.reads.ReadShardStrategy.advance(ReadShardStrategy.java:176)
> at
> org.broadinstitute.sting.gatk.datasources.reads.ReadShardStrategy.next(ReadShardStrategy.java:126)
> at
> org.broadinstitute.sting.gatk.datasources.reads.ReadShardStrategy.next(ReadShardStrategy.java:41)
> at
> org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator$1.doBody(GenomeLocProcessingTracker.java:261)
> at
> org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator$1.doBody(GenomeLocProcessingTracker.java:253)
> at
> org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$WithLock.run(GenomeLocProcessingTracker.java:426)
> at
> org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator.next(GenomeLocProcessingTracker.java:253)
> at
> org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator.next(GenomeLocProcessingTracker.java:216)
> at
> org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:53)
> at
> org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234)
> at
> org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
> at
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
> at
> org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)
> Caused by: java.io.IOException: Invalid file pointer: 71767958683648
> at
> net.sf.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:220)
> at
> net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:590)
> at
> net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:460)
> ... 18 more
> ##### ERROR
> ------------------------------------------------------------------------------------------
> ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165):
> ##### ERROR
> ##### ERROR Please visit the 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: Invalid file pointer: 71767958683648
> ##### ERROR
> ------------------------------------------------------------------------------------------
>
> Could anyone please help? Thank you in advance.
>
> Andrew
>
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