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Samebug tips

  1. ,

    If the directory ../.foo/bar/ doesn't exist, you can't create a file there, so make sure you create the directory first.

    File f = new File("somedirname1/somedirname2/somefilename");
    if (!f.getParentFile().exists())
        f.getParentFile().mkdirs();
    

Solutions on the web

via GitHub by yhoogstrate
, 1 year ago
Exception creating temporary directory.
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Exception creating temporary directory.
via usegalaxy.org by Unknown author, 1 year ago
Exception creating temporary directory.
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Exception creating temporary directory.
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Exception creating temporary directory.
via GitHub by olegs
, 4 months ago
Could not create temporary directory /tmp/3481979.mgt2.cluster/CSPI.8518873774469239343.tmp
java.io.IOException: Permission denied	at java.io.UnixFileSystem.createFileExclusively(Native Method)	at java.io.File.createNewFile(File.java:1006)	at java.io.File.createTempFile(File.java:1989)	at java.io.File.createTempFile(File.java:2040)	at htsjdk.samtools.util.IOUtil.createTempDir(IOUtil.java:668)	at htsjdk.samtools.CoordinateSortedPairInfoMap.(CoordinateSortedPairInfoMap.java:59)	at picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.(DiskBasedReadEndsForMarkDuplicatesMap.java:57)	at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:250)	at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:114)	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)