SAMFormatException: Did not inflate expected amount error

0

I am facing an error while running GATK Basecalibrator.

[1 July 2021 at 5:00:42 PM IST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 35.00 minutes.
Runtime.totalMemory()=791674880
htsjdk.samtools.SAMFormatException: Did not inflate expected amount
    at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:147)
    at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
    at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
    at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
    at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
    at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
    at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
    at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:241)
    at htsjdk.tribble.readers.TabixReader.readLine(TabixReader.java:215)
    at htsjdk.tribble.readers.TabixReader.access$300(TabixReader.java:48)
    at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:434)
    at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:46)
    at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:170)
    at htsjdk.tribble.TabixFeatureReader$FeatureIterator.<init>(TabixFeatureReader.java:159)
    at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:133)
    at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:569)
    at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:538)
    at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:352)
    at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:173)
    at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:125)
    at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:263)
    at org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator.apply(BaseRecalibrator.java:189)
    at org.broadinstitute.hellbender.engine.ReadWalker.lambda$traverse$0(ReadWalker.java:96)
    at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
    at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
    at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)
    at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
    at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
    at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
    at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
    at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
    at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
    at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
    at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
    at org.broadinstitute.hellbender.engine.ReadWalker.traverse(ReadWalker.java:94)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1058)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
    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)

What does this mean? Is it related to memory? My system has 16 GB memory, still it is giving me this error again and again. What to do to get rid of this?


WES

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