Question: MarkDuplicates error for RNA-Seq
0
gravatar for KG
7 months ago by
KG0
KG0 wrote:

Hi, I am trying to run MarkDuplicates but keep getting the error listed below, although I added the TMP_DIR=yourdirectory/tmp in command line.

Please advice Thanks a bunch!

**Command**
 *java -jar MarkDuplicates.jar INPUT= Read_sorted.bam OUTPUT=Read_sortremove.bam METRICS_FILE=metrics.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT TMP_DIR=yourdirectory/tmp*


**Error**
----------
Exception in thread "main" htsjdk.samtools.SAMException: /home/as/SNPiR/yourdirectory/tmp/CSPI.1714605993024191960.tmp/13316.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.DiskReadEndsMap.put(DiskReadEndsMap.java:67)
    at picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:449)
    at picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:177)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
    at picard.sam.MarkDuplicates.main(MarkDuplicates.java:161)
Caused by: java.io.FileNotFoundException: /home/as/SNPiR/yourdirectory/tmp/CSPI.1714605993024191960.tmp/13316.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)
rna-seq software error • 234 views
ADD COMMENTlink modified 7 months ago by genomax64k • written 7 months ago by KG0

Normally there is no need to mark/remove duplicates in RNAseq data.

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax64k

Picard is not finding the temporary directory:

Exception in thread "main" htsjdk.samtools.SAMException: /home/as/SNPiR/yourdirectory/tmp/CSPI.1714605993024191960.tmp/13316.tmpnot found

But listen to genomax suggestion, probably there is no need to mark/remove duplicates in your data.

ADD REPLYlink written 7 months ago by h.mon24k
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