Question: picard MarkDuplicates error
0
gravatar for Cindy
18 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 • 567 views
ADD COMMENTlink modified 18 months ago by genomax60k • written 18 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 18 months ago • written 18 months ago by genomax60k
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 18 months ago by Pierre Lindenbaum116k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1573 users visited in the last hour