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Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

The error of Mark Dupplicate

I run the step of Mark Duplicate in the server, but it always print an error message even though I changed server.
This is my input:
java -jar /home/yangguoqian/biosoft/picard-tools-2.5.0/picard.jar MarkDuplicates INPUT=/home/chenyunmei/hetero/moso_gatk/bam/Bamboo-PCRfree_Round68_Lane1.bam OUTPUT=/home/chenyunmei/hetero/moso_gatk/markDup/Bamboo-PCRfree_Round68_Lane1.dedupped.bam METRICS_FILE=/home/chenyunmei/hetero/moso_gatk/markDup/Bamboo-PCRfree_Round68_Lane1.dedupped.metrics.txt VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true REMOVE_DUPLICATES=TRUE

And the follow is the error message:
optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Sat Jul 30 19:56:01 CST 2016] Executing as chenyunmei@localhost.localdomain on Linux 3.10.0-229.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_77-b03; Picard version: 2.5.0(2c370988aefe41f579920c8a6a678a201c5261c1_1466708365)
INFO 2016-07-30 19:56:01 MarkDuplicates Start of doWork freeMemory: 2045995552; totalMemory: 2058354688; maxMemory: 28631367680
INFO 2016-07-30 19:56:01 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-07-30 19:56:01 MarkDuplicates Will retain up to 110120644 data points before spilling to disk.
[Sat Jul 30 19:56:12 CST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.18 minutes.
To get help, see
Exception in thread "main" htsjdk.samtools.SAMException: /tmp/chenyunmei/CSPI.2016309087006492130.tmp/150462.tmpnot found
at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(
at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(
at htsjdk.samtools.util.ResourceLimitedMap.get(
at htsjdk.samtools.CoordinateSortedPairInfoMap.getOutputStreamForSequence(
at htsjdk.samtools.CoordinateSortedPairInfoMap.put(
at picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.put(
at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(
at picard.sam.markduplicates.MarkDuplicates.doWork(
at picard.cmdline.CommandLineProgram.instanceMain(
at picard.cmdline.PicardCommandLine.instanceMain(
at picard.cmdline.PicardCommandLine.main(
Caused by: /tmp/chenyunmei/CSPI.2016309087006492130.tmp/150462.tmp (Too many open files)
at Method)
at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(
... 10 more

Please help me. I have waste a lot of time in this, but I really don't know what is the reason.


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