When running RevertSam (4.0.1.2), I get the following "File to large" error.
The bam file is only 109GB. Any suggestions?
gatk --java-options "-Djava.io.tmpdir=tmp -Xmx64G" RevertSam\
-I $BAM_FILE \
-O ubam/$BAM \
--OUTPUT_BY_READGROUP true\
--SANITIZE true \
--MAX_DISCARD_FRACTION 0.005 \
--ATTRIBUTE_TO_CLEAR XT \
--ATTRIBUTE_TO_CLEAR XN \
--ATTRIBUTE_TO_CLEAR AS \
--ATTRIBUTE_TO_CLEAR OC \
--ATTRIBUTE_TO_CLEAR OP \
--SORT_ORDER=queryname \
--RESTORE_ORIGINAL_QUALITIES true \
--REMOVE_DUPLICATE_INFORMATION true \
--REMOVE_ALIGNMENT_INFORMATION true
htsjdk.samtools.util.RuntimeIOException: java.io.IOException: File too large
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:247)
at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:167)
at picard.sam.RevertSam$RevertSamSorter.add(RevertSam.java:706)
at picard.sam.RevertSam.doWork(RevertSam.java:307)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:269)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:159)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:202)
at org.broadinstitute.hellbender.Main.main(Main.java:288)
Caused by: java.io.IOException: File too large
at sun.nio.ch.FileDispatcherImpl.write0(Native Method)
at sun.nio.ch.FileDispatcherImpl.write(FileDispatcherImpl.java:60)
at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:93)
at sun.nio.ch.IOUtil.write(IOUtil.java:65)
at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:211)
at java.nio.channels.Channels.writeFullyImpl(Channels.java:78)
at java.nio.channels.Channels.writeFully(Channels.java:101)
at java.nio.channels.Channels.access$000(Channels.java:61)
at java.nio.channels.Channels$1.write(Channels.java:174)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
at org.xerial.snappy.SnappyOutputStream.dumpOutput(SnappyOutputStream.java:360)
at org.xerial.snappy.SnappyOutputStream.compressInput(SnappyOutputStream.java:374)
at org.xerial.snappy.SnappyOutputStream.flush(SnappyOutputStream.java:334)
at org.xerial.snappy.SnappyOutputStream.close(SnappyOutputStream.java:397)
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:238)