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Problem in running Picard RevertSam

MUHAMMADSOHAILRAZAMUHAMMADSOHAILRAZA Beijing Institute of Genomics, CASMember ✭✭

Dear Picard/GATK teams,
I am using Picard v2.2.4 RevertSam tool. My command-line was:

java -Djava.io.tmpdir=$TMP -Xmx30g -jar picard.jar RevertSam \
I=LP6005441-DNA_B07.modRG.bam \
O=LP6005441-DNA_B07-revertsam.bam \
SANITIZE=true \
MAX_DISCARD_FRACTION=0.005 \
ATTRIBUTE_TO_CLEAR=NM \
ATTRIBUTE_TO_CLEAR=MD \
ATTRIBUTE_TO_CLEAR=AS \
ATTRIBUTE_TO_CLEAR=XS \
ATTRIBUTE_TO_CLEAR=SA \
ATTRIBUTE_TO_CLEAR=XA \
SORT_ORDER=queryname \
RESTORE_ORIGINAL_QUALITIES=true \
REMOVE_DUPLICATE_INFORMATION=true \
REMOVE_ALIGNMENT_INFORMATION=true

I am getting the following error message,
ERROR
Runtime.totalMemory()=9180807168
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Input/output error
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:246)
at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:166)
at picard.sam.RevertSam.doWork(RevertSam.java:233)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Caused by: java.io.IOException: Input/output error
at java.io.FileOutputStream.close0(Native Method)
at java.io.FileOutputStream.access$000(FileOutputStream.java:53)
at java.io.FileOutputStream$1.close(FileOutputStream.java:356)
at java.io.FileDescriptor.closeAll(FileDescriptor.java:212)
at java.io.FileOutputStream.close(FileOutputStream.java:354)
at java.io.FilterOutputStream.close(FilterOutputStream.java:159)
at org.xerial.snappy.SnappyOutputStream.close(SnappyOutputStream.java:140)
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:237)

can anyone please help me to resolve this issue.
.

Thanks!

Answers

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