error when running MarkDuplicates

Question

[kk.mahsa]

when i run Picard to mark duplicates i get this error:

To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMException: /tmp/CSPI.61127736197136018.tmp/7237.tmpnot found at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(FileAppendStreamLRUCache.java:63) at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(FileAppendStreamLRUCache.java:49) at htsjdk.samtools.util.ResourceLimitedMap.get(ResourceLimitedMap.java:76) at htsjdk.samtools.CoordinateSortedPairInfoMap.getOutputStreamForSequence(CoordinateSortedPairInfoMap.java:180) at htsjdk.samtools.CoordinateSortedPairInfoMap.put(CoordinateSortedPairInfoMap.java:164) at picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.put(DiskBasedReadEndsForMarkDuplicatesMap.java:65) at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:478) at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:222) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105) Caused by: java.io.FileNotFoundException: /tmp/CSPI.61127736197136018.tmp/7237.tmp (Too many open files) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.<init>(FileOutputStream.java:213) at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(FileAppendStreamLRUCache.java:60) ... 10 more

---

used command to do marking was:

Picard$ java -Xmx25G -jar picard.jar MarkDuplicates \

I= /home/MyLinux/Downloads/Sorted_Merged.bam \

O= /home/MyLinux/Downloads/dedupD1.bam \

M= /home/MyLinux/Downloads/dedup_Metrics.txt \

REMOVE_DUPLICATES=true \

TMP_DIR=/tmp

anybody can help me to resolve this error?

Answer 1

[John]

You've got a (Too many open files) error - either someone over at the Picard development team forgot to close the files they're opening, or your OS is not giving Picard enough resources to do its job - one of those resources being how many files a program can read/write simultaneously.

[kk.mahsa]

what is sulotion? anbody can help me?

[John]

Sorry kk, it's not really a bioinformatics problem, it's a computer problem. I would talk to whomever operates your IT system, or perhaps try and share the data with the Picard team to see if they also get the same problem?