Question: picard MarkDuplicates error
gravatar for Cindy
12 months ago by
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.sam.CoordinateSortedPairInfoMap.<init>(
    at net.sf.picard.sam.DiskReadEndsMap.<init>(
    at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(
    at net.sf.picard.sam.MarkDuplicates.doWork(
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(
    at net.sf.picard.sam.MarkDuplicates.main(
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

this doesn't exist anymore. It's now


it means that your version of picard is very old. current is 2.10.3

ADD REPLYlink written 12 months ago by Pierre Lindenbaum110k
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