The temporary BioPAX and text files created by the cpath2 queries/converter are not always removed (perhaps due to internal errors), and the files generated with paxtools' json-converter are not removed until the JVM exits.
The temporary directory (java.io.tmpdir) is (if cpath2 was run using the exec-jar with built-in Tomcat):
$CPATH2_HOME/.extract/temp. The file names look like cpath2_owl (_txt) or biopaxTmp*owl.
The temporary BioPAX and text files created by the cpath2 queries/converter are not always removed (perhaps due to internal errors), and the files generated with paxtools' json-converter are not removed until the JVM exits.
The temporary directory (java.io.tmpdir) is (if cpath2 was run using the exec-jar with built-in Tomcat): $CPATH2_HOME/.extract/temp. The file names look like cpath2_owl (_txt) or biopaxTmp*owl.