Picard "no space left on device" error

Sometimes Picard's tools terminate with the error message  "no space left on device" even though there is plenty of space available on the disk.

In addition Picard will throw some java exception error messages such as:
Exception in thread "main" net.sf.samtools.util.RuntimeIOException: Write error;
.
.
Caused by: java.io.IOException: Input/output error
    at java.io.FileOutputStream.writeBytes(Native Method)
    at java.io.FileOutputStream.write(FileOutputStream.java:297)
    at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:197)
.
.
etc.


By default Picard tries to use system's temporary directory which has a limited space allocated to it by the system. If you are working with very large data files, then the default temporary directory gets filled up quickly and Picard stops working.
To avoid this error message you create a temporary directory somewhere on your system and direct picard to use that as temporary directory. Specify TMP_DIR=/some_path/your_temporary_directory/