Question: picard MarkDuplicates error
0
gravatar for Cindy
12 months ago by
Cindy20
Cindy20 wrote:

Hi, I have got a wired error from picard. When I run MarkDuplicates for single file, it works. But when I run multiple files, it shows error as following. Is this because too many files? or something wrong with the virtual box? I am running thin on Ubuntu on VM (host: win 10)

Exception in thread "main" net.sf.picard.PicardException: Could not create temporary directory /tmp/CSPI.3839395324178121807.tmp
    at net.sf.picard.io.IoUtil.createTempDir(IoUtil.java:476)
    at net.sf.picard.sam.CoordinateSortedPairInfoMap.<init>(CoordinateSortedPairInfoMap.java:51)
    at net.sf.picard.sam.DiskReadEndsMap.<init>(DiskReadEndsMap.java:57)
    at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:391)
    at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:161)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
    at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:145)
sequencing • 423 views
ADD COMMENTlink modified 12 months ago by genomax52k • written 12 months ago by Cindy20

But when I run multiple files

What does your Picard command look like in that case? The error is about not being able to create directories in the /tmp directory.

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax52k
at net.sf.picard.io.IoUtil.createTempDir(IoUtil.java:476)

this doesn't exist anymore. It's now

htsjdk.samtools.util.IOUtil

it means that your version of picard is very old. current is 2.10.3 https://github.com/broadinstitute/picard/releases

ADD REPLYlink written 12 months ago by Pierre Lindenbaum110k
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