java.io.IOException: Input/output error
REQUIRED for all errors and issues:
a) GATK version used:gatk-4.4.0.0
b) Exact command used:/opt/biosoft/gatk-4.4.0.0/gatk HaplotypeCaller -R genome.fasta -I LSL1.MD.bam -ERC GVCF -O LSL1_test.g.vcf --pcr-indel-model CONSERVATIVE --sample-ploidy 2 --min-base-quality-score 10 --kmer-size 10 --kmer-size 25 &
c) Entire program log:
Dear GATK team:
I am using gatk-4.4.0.0 to get gVCF files. After it runs, I see the outputted intermediate gVCF file; however, I also see that it failed to run. The error log is as following:
16:41:18.277 INFO HaplotypeCaller - Shutting down engine
[4:41:18] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 2,543.94 minutes.
Runtime.totalMemory()=11156848640
htsjdk.samtools.SAMException: Unable to load ptg002394l(0, 206650) from /disks/node7_RAID6_120TB/home/yanyujie/05-resequence/04.variants_calling/GATK/genome.fasta
at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:207)
at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:340)
at org.broadinstitute.hellbender.engine.AssemblyRegion.getReference(AssemblyRegion.java:368)
at org.broadinstitute.hellbender.engine.AssemblyRegion.getAssemblyRegionReference(AssemblyRegion.java:391)
at org.broadinstitute.hellbender.engine.AssemblyRegion.getAssemblyRegionReference(AssemblyRegion.java:377)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils.createReferenceHaplotype(AssemblyBasedCallerUtils.java:242)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.referenceModelForNoVariation(HaplotypeCallerEngine.java:901)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:605)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:271)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:200)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.io.IOException: Input/Output error
at java.base/sun.nio.ch.FileDispatcherImpl.pread0(Native Method)
at java.base/sun.nio.ch.FileDispatcherImpl.pread(FileDispatcherImpl.java:54)
at java.base/sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:328)
at java.base/sun.nio.ch.IOUtil.read(IOUtil.java:296)
at java.base/sun.nio.ch.IOUtil.read(IOUtil.java:273)
at java.base/sun.nio.ch.FileChannelImpl.readInternal(FileChannelImpl.java:839)
at java.base/sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:824)
at htsjdk.samtools.reference.IndexedFastaSequenceFile.readFromPosition(IndexedFastaSequenceFile.java:148)
at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:204)
... 18 more
~
And when I used a small genome to test, it is successful to form gVCF files.
Thank you for your help!
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Hi yujie yan
Given the fact that a smaller reference genome works but a larger one does not tells me that there is an IO bottleneck/issue/permission problem etc. present that prevents GATK to reach that resource properly. Can you localize your files to the server directly if those files are only present on an NFS/SMB partition and see if that works?
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