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Stream closed error with gatk 4.1.1.0

fazulurfazulur hyderabadMember

Dear GATK team,

I am getting the below error when running gatk-variant pipeline of bcbio. Bcbio using gatk 4.1.1.0 version.
When I run ApplyBQSRSpark using GATK 4.0.9.0, it runs fine without any issues.

Here is the command
**
gatk ApplyBQSRSpark --input test-sort.bam --output test-sort-recal.bam --bqsr-recal-file test-sort-recal.grp --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 --spark-master local[8] --conf spark.local.dir=scratch/ --conf spark.driver.host=localhost --conf spark.network.timeout=800 --jdk-deflater --jdk-inflater**

Here is the error

[April 28, 2019 10:11:25 AM AST] org.broadinstitute.hellbender.tools.spark.ApplyBQSRSpark done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=874512384
htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed
at htsjdk.samtools.IndexStreamBuffer.readFully(IndexStreamBuffer.java:23)
at htsjdk.samtools.IndexStreamBuffer.readLong(IndexStreamBuffer.java:62)
at htsjdk.samtools.AbstractBAMFileIndex.readLong(AbstractBAMFileIndex.java:436)
at htsjdk.samtools.AbstractBAMFileIndex.query(AbstractBAMFileIndex.java:311)
at htsjdk.samtools.CachingBAMFileIndex.getQueryResults(CachingBAMFileIndex.java:159)
at htsjdk.samtools.BAMIndexMerger.processIndex(BAMIndexMerger.java:43)
at htsjdk.samtools.BAMIndexMerger.processIndex(BAMIndexMerger.java:16)
at org.disq_bio.disq.impl.file.IndexFileMerger.mergeParts(IndexFileMerger.java:90)
at org.disq_bio.disq.impl.formats.bam.BamSink.save(BamSink.java:132)
at org.disq_bio.disq.HtsjdkReadsRddStorage.write(HtsjdkReadsRddStorage.java:225)
at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink.writeReads(ReadsSparkSink.java:155)
at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink.writeReads(ReadsSparkSink.java:120)
at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.writeReads(GATKSparkTool.java:361)
at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.writeReads(GATKSparkTool.java:349)
at org.broadinstitute.hellbender.tools.spark.ApplyBQSRSpark.runTool(ApplyBQSRSpark.java:90)
at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:528)
at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:30)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: java.io.IOException: Stream closed
at java.io.BufferedInputStream.getBufIfOpen(BufferedInputStream.java:170)
at java.io.BufferedInputStream.read(BufferedInputStream.java:336)
at java.io.DataInputStream.read(DataInputStream.java:149)
at java.io.DataInputStream.read(DataInputStream.java:149)
at org.disq_bio.disq.impl.file.HadoopFileSystemWrapper$SeekableHadoopStream.read(HadoopFileSystemWrapper.java:232)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:246)
at java.io.BufferedInputStream.read1(BufferedInputStream.java:286)
at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
at htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:133)
at htsjdk.samtools.IndexStreamBuffer.readFully(IndexStreamBuffer.java:21)
... 22 more
19/04/28 10:11:25 INFO ShutdownHookManager: Shutdown hook called

Could you please help me to resolve this issue.

Thanks In Advance
Fazulur Rehaman

Issue · Github
by bhanuGandham

Issue Number
5919
State
open
Last Updated

Answers

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