If transformation is like below,
<transformation name="getSortedWords">
   <uses name="getSortedWords" executable="true"/>
   <uses name="io.sh" executable="true"/>
   <uses name="test.txt"/>
</transformation>

File test.txt is defined in RC like below,
<file name="test.txt">
   <pfn url="file:///.../test.txt"/>
</file>

I get an exception like,
[FATAL ERROR] java.lang.RuntimeException: There are no entries for the transformation "test.txt" in the TC
at edu.isi.pegasus.planner.catalog.transformation.mapper.All.getSiteMap(All.java:106)
at edu.isi.pegasus.planner.catalog.transformation.Mapper.getTCList(Mapper.java:175)
at edu.isi.pegasus.planner.refiner.InterPoolEngine.handleFileTransfersForDependantExecutables(InterPoolEngine.java:633)
at edu.isi.pegasus.planner.refiner.InterPoolEngine.handleExecutableFileTransfers(InterPoolEngine.java:506)
at edu.isi.pegasus.planner.refiner.InterPoolEngine.scheduleJobs(InterPoolEngine.java:323)
at edu.isi.pegasus.planner.refiner.InterPoolEngine.determineSites(InterPoolEngine.java:213)
at edu.isi.pegasus.planner.refiner.MainEngine.runPlanner(MainEngine.java:187)
at edu.isi.pegasus.planner.client.CPlanner.executeCommand(CPlanner.java:644)
at edu.isi.pegasus.planner.client.CPlanner.executeCommand(CPlanner.java:365)
at edu.isi.pegasus.planner.client.CPlanner.main(CPlanner.java:246)