CombineGVCFs ERROR:java.lang.RuntimeException: java.io.IOException: Input/output error

tenghtengh chinaMember

Hi guys!
When I run the GATK to combine several gvcf files using the follwing command:
"java -XX:ParallelGCThreads=6 -Xmx50g -Djava.io.tmpdir=/SNP/tmp -jar /GenomeAnalysisTK/3.2-2/GenomeAnalysisTK.jar -T CombineGVCFs -R ref.fa -V bam.1.gvcf -V bam.2.gvcf -V bam.3.gvcf -V bam.4.gvcf -V bam.5.gvcf -o bam.gvcf"
But the following error infomation is given. SO what should I do with this problem?

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.RuntimeException: java.io.IOException: Input/output error
at htsjdk.tribble.readers.LineReaderUtil$1.readLine(LineReaderUtil.java:47)
at htsjdk.tribble.readers.LineIteratorImpl.advance(LineIteratorImpl.java:23)
at htsjdk.tribble.readers.LineIteratorImpl.advance(LineIteratorImpl.java:10)
at htsjdk.samtools.util.AbstractIterator.hasNext(AbstractIterator.java:44)
at htsjdk.tribble.AsciiFeatureCodec.isDone(AsciiFeatureCodec.java:53)
at htsjdk.tribble.AsciiFeatureCodec.isDone(AsciiFeatureCodec.java:41)
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.
java:424)
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.(TribbleIndexedFeatureReader.java:367)
at htsjdk.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:236)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack.query(RMDTrack.java:119)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResou:
rce(ReferenceOrderedDataSource.java:241)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:185)
at org.broadinstitute.gatk.engine.datasources.rmd.ResourcePool.iterator(ResourcePool.java:93)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.seek(ReferenceOrderedDataSource.java:168)
at org.broadinstitute.gatk.engine.datasources.providers.RodLocusView.(RodLocusView.java:83)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.getLocusView(TraverseLociNano.java:129)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:80)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
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:107)
Caused by: java.io.IOException: Input/output error
at java.io.RandomAccessFile.readBytes0(Native Method)
at java.io.RandomAccessFile.readBytes(RandomAccessFile.java:350)
at java.io.RandomAccessFile.read(RandomAccessFile.java:385)
at htsjdk.samtools.seekablestream.SeekableFileStream.read(SeekableFileStream.java:80)
at htsjdk.tribble.TribbleIndexedFeatureReader$BlockStreamWrapper.read(TribbleIndexedFeatureReader.java:517)
at java.io.InputStream.read(InputStream.java:101)
at htsjdk.tribble.readers.PositionalBufferedStream.fill(PositionalBufferedStream.java:127)
at htsjdk.tribble.readers.PositionalBufferedStream.read(PositionalBufferedStream.java:79)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:283)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:325)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:177)
at java.io.InputStreamReader.read(InputStreamReader.java:184)
at htsjdk.tribble.readers.LongLineBufferedReader.fill(LongLineBufferedReader.java:140)
at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:298)
at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:354)
at htsjdk.tribble.readers.LineReaderUtil$1.readLine(LineReaderUtil.java:45)
... 23 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
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: java.io.IOException: Input/output error
ERROR --------------------------------------------------------------------------------

Answers

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