picard MarkDuplicates error
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)
• 2,385 views
•
link
0 answers
No answers yet.
Log in to answer this question.
What does your Picard command look like in that case? The error is about not being able to create directories in the /tmp directory.
this doesn't exist anymore. It's now
it means that your version of picard is very old. current is 2.10.3 https://github.com/broadinstitute/picard/releases