[svtoolkit-help] Invalid file pointer
Status: Beta
Brought to you by:
bhandsaker
Menu
▾
▴
[svtoolkit-help] Invalid file pointer
|
From: yw <yw...@gm...> - 2012-10-06 07:33:08
|
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 |
