htsjdk.samtools.SAMException

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    • htsjdk.samtools.SAMException: Exception creating temporary directory. at htsjdk.samtools.util.IOUtil.createTempDir(IOUtil.java:677) at htsjdk.samtools.CoordinateSortedPairInfoMap.<init>(CoordinateSortedPairInfoMap.java:59) at picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.<init>(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) Caused by: 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) ... 7 more

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