Re: [Samtools-help] picard_MarkDuplicates:Exception closing FileOutputStream

[Thomas S. <trs...@uw...>]

On Sep 29, 2014, at 22:13 , Mengmeng Lu <mir...@ta...> 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