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picard downsampling cram files failed!

Dear GATK,

I am trying to conduct downsampling on our cram file. However, the run failed!

Here is the command line I used:
java -Xmx16G -jar /software/picard.jar DownsampleSam I=H2NCHCCXY-7.hgv.cram O=ds.cram P=0.2 R=12345 REFERENCE_SEQUENCE=/next-gen/Illumina/bwa_references/g/GRCh38_1000Genomes/GRCh38_full_analysis_set.fa

the java version is jdk1.8.0_74

The Picard version is: 2.10.6

the error messages:
ERROR 2017-08-01 15:22:35 Slice Reference MD5 mismatch for slice 0:248733152-248765543, CACAGATTCT...TGATTATCTC
[Tue Aug 01 15:22:35 CDT 2017] picard.sam.DownsampleSam done. Elapsed time: 9.41 minutes.
Runtime.totalMemory()=2226126848
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.cram.CRAMException: Reference sequence MD5 mismatch for slice: sequence id 0, start 248733152, span 32392, expected MD5 83849184708b9131cb455f52e70da52d
at htsjdk.samtools.CRAMIterator.nextContainer(CRAMIterator.java:187)
at htsjdk.samtools.CRAMIterator.hasNext(CRAMIterator.java:261)
at htsjdk.samtools.SamReader$AssertingIterator.hasNext(SamReader.java:601)
at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:70)
at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57)
at htsjdk.samtools.ConstantMemoryDownsamplingIterator.next(ConstantMemoryDownsamplingIterator.java:83)
at htsjdk.samtools.ConstantMemoryDownsamplingIterator.next(ConstantMemoryDownsamplingIterator.java:44)
at picard.sam.DownsampleSam.doWork(DownsampleSam.java:127)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:228)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)

I searched the internet and wasn't able to find the solution. Please help! Thanks!

Best,

Peter

Answers

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