How can I fix the following error in BQSR

I used the following script:

java -Xmx5g -jar $gatk -T BaseRecalibrator -R $ref_dir/ucsc.hg19.fasta -I $bam_dir/T-SZ-03-1_NHDE0249-11_C3AP0ACXX_L3.dedupped.realigned.bam -knownSites $ref_dir/dbsnp_138.hg19.vcf -knownSites $ref_dir/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -knownSites $ref_dir/1000G_phase1.indels.hg19.sites.vcf -o $other_dir/T-SZ-03-1_NHDE0249-11_C3AP0ACXX_L3.recal.grp

java -Xmx5g -jar $gatk -T BaseRecalibrator -R $ref_dir/ucsc.hg19.fasta -I $bam_dir/T-SZ-03-1_NHDE0249-11_C3AP0ACXX_L3.dedupped.realigned.bam -BQSR $other_dir/T-SZ-03-1_NHDE0249-11_C3AP0ACXX_L3.recal.grp -o $other_dir/T-SZ-03-1_NHDE0249-11_C3AP0ACXX_L3.post.recal.grp -knownSites $ref_dir/dbsnp_138.hg19.vcf -knownSites $ref_dir/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -knownSites $ref_dir/1000G_phase1.indels.hg19.sites.vcf

java -Xmx5g -jar $gatk -T AnalyzeCovariates -R $ref_dir/ucsc.hg19.fasta -before $other_dir/T-SZ-03-1_NHDE0249-11_C3AP0ACXX_L3.recal.grp -after $other_dir/T-SZ-03-1_NHDE0249-11_C3AP0ACXX_L3.post.recal.grp -plots $other_dir/T-SZ-03-1_NHDE0249-11_C3AP0ACXX_L3.recalibration_plots.pdf

java -Xmx5g -jar $gatk -T PrintReads -R $ref_dir/ucsc.hg19.fasta -I $bam_dir/T-SZ-03-1_NHDE0249-11_C3AP0ACXX_L3.dedupped.realigned.bam -BQSR $other_dir/T-SZ-03-1_NHDE0249-11_C3AP0ACXX_L3.recal.grp -o $bam_dir/T-SZ-03-1_NHDE0249-11_C3AP0ACXX_L3.dedupped.realigned.recal.bam

The I got the following error message for the first step:

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

java.lang.RuntimeException: java.io.IOException: Input/output error
at htsjdk.tribble.readers.AsciiLineReaderIterator$TupleIterator.advance(AsciiLineReaderIterator.java:87)
at htsjdk.tribble.readers.AsciiLineReaderIterator$TupleIterator.advance(AsciiLineReaderIterator.java:74)
at htsjdk.samtools.util.AbstractIterator.next(AbstractIterator.java:57)
at htsjdk.tribble.readers.AsciiLineReaderIterator.next(AsciiLineReaderIterator.java:47)
at htsjdk.tribble.readers.AsciiLineReaderIterator.next(AsciiLineReaderIterator.java:25)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41)
at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:40)
at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:478)
at htsjdk.tribble.index.IndexFactory$FeatureIterator.next(IndexFactory.java:440)
at htsjdk.tribble.index.IndexFactory.createIndex(IndexFactory.java:338)
at htsjdk.tribble.index.IndexFactory.createDynamicIndex(IndexFactory.java:312)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:402)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:288)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:225)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:148)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.(ReferenceOrderedDataSource.java:208)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.(ReferenceOrderedDataSource.java:88)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:997)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:779)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:290)
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.FileInputStream.readBytes(Native Method)
at java.io.FileInputStream.read(FileInputStream.java:224)
at htsjdk.tribble.readers.PositionalBufferedStream.fill(PositionalBufferedStream.java:127)
at htsjdk.tribble.readers.PositionalBufferedStream.peek(PositionalBufferedStream.java:118)
at htsjdk.tribble.readers.PositionalBufferedStream.read(PositionalBufferedStream.java:57)
at htsjdk.tribble.readers.AsciiLineReader.readLine(AsciiLineReader.java:80)
at htsjdk.tribble.readers.AsciiLineReader.readLine(AsciiLineReader.java:122)
at htsjdk.tribble.readers.AsciiLineReaderIterator$TupleIterator.advance(AsciiLineReaderIterator.java:85)
... 24 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af):
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
Tagged:

Best Answers

Answers

  • pkuyhpkuyh pkuMember
    edited March 2015

    @Geraldine_VdAuwera said:
    Hi there,

    This looks like it might be an issue with your input VCF files. Try running ValidateVariants on each file individually.

    thx.
    i tried every vcf files and all of them got the same error message just like the feedback info from BQSR.
    i paste one of them there.

    INFO 13:22:58,570 HelpFormatter - --------------------------------------------------------------------------------
    INFO 13:22:58,572 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
    INFO 13:22:58,572 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 13:22:58,572 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 13:22:58,575 HelpFormatter - Program Args: -R /media/LAB636/01.06.job/Ref/ucsc.hg19.fasta -T ValidateVariants --variant /media/LAB636/01.06.job/Ref/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf --dbsnp /media/LAB636/01.06.job/Ref/dbsnp_138.hg19.vcf
    INFO 13:22:58,584 HelpFormatter - Executing as [email protected] on Linux 2.6.32-38-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13.
    INFO 13:22:58,585 HelpFormatter - Date/Time: 2015/03/18 13:22:58
    INFO 13:22:58,585 HelpFormatter - --------------------------------------------------------------------------------
    INFO 13:22:58,585 HelpFormatter - --------------------------------------------------------------------------------
    INFO 13:22:58,938 GenomeAnalysisEngine - Strictness is SILENT
    INFO 13:22:59,012 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000

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

    java.lang.RuntimeException: java.io.IOException: Input/output error
    at htsjdk.tribble.readers.AsciiLineReaderIterator$TupleIterator.advance(AsciiLineReaderIterator.java:87)
    at htsjdk.tribble.readers.AsciiLineReaderIterator$TupleIterator.advance(AsciiLineReaderIterator.java:74)
    at htsjdk.samtools.util.AbstractIterator.next(AbstractIterator.java:57)
    at htsjdk.tribble.readers.AsciiLineReaderIterator.next(AsciiLineReaderIterator.java:47)
    at htsjdk.tribble.readers.AsciiLineReaderIterator.next(AsciiLineReaderIterator.java:25)
    at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79)
    at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41)
    at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:40)
    at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:478)
    at htsjdk.tribble.index.IndexFactory$FeatureIterator.next(IndexFactory.java:440)
    at htsjdk.tribble.index.IndexFactory.createIndex(IndexFactory.java:338)
    at htsjdk.tribble.index.IndexFactory.createDynamicIndex(IndexFactory.java:312)
    at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:402)
    at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:288)
    at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:225)
    at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:148)
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.(ReferenceOrderedDataSource.java:208)
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.(ReferenceOrderedDataSource.java:88)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:997)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:779)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:290)
    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.FileInputStream.readBytes(Native Method)
    at java.io.FileInputStream.read(FileInputStream.java:224)
    at htsjdk.tribble.readers.PositionalBufferedStream.fill(PositionalBufferedStream.java:127)
    at htsjdk.tribble.readers.PositionalBufferedStream.peek(PositionalBufferedStream.java:118)
    at htsjdk.tribble.readers.PositionalBufferedStream.read(PositionalBufferedStream.java:57)
    at htsjdk.tribble.readers.AsciiLineReader.readLine(AsciiLineReader.java:80)
    at htsjdk.tribble.readers.AsciiLineReader.readLine(AsciiLineReader.java:122)
    at htsjdk.tribble.readers.AsciiLineReaderIterator$TupleIterator.advance(AsciiLineReaderIterator.java:85)
    ... 24 more

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af):
    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 ------------------------------------------------------------------------------------------
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