On Sep 29, 2014, at 22:13 , Mengmeng Lu <mira0...@tamu.edu> wrote: > Exception in thread "main" htsjdk.samtools.SAMException: Exception closing > FileOutputStream for > /data/mira0501/agilentfastq/nonmulti/mira0501/CSPI.5751822609546779855.t > mp/27421.tmp
I bet you're running out of disk space for the temporary files Picard uses during MarkDuplicates. How much disk space is available? You can specify an alternate directory for temporary files (perhaps on a partition/drive with more space) using the TMP_DIR=/some/path option. Thomas ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
