My submit host got messed up and we had to reboot it. When I tried to resubmit some of the workflows I got this error:

$ pegasus-run $PWD
Rescued /submit/kepler2012/work/gideon/pegasus/Run2-25/run0001/Run2-25-0.log as /submit/kepler2012/work/gideon/pegasus/Run2-25/run0001/Run2-25-0.log.000

ERROR: "Run2-25-0.dag.condor.sub" already exists.
ERROR: "Run2-25-0.dag.lib.out" already exists.
ERROR: "Run2-25-0.dag.lib.err" already exists.
ERROR: "Run2-25-0.dag.dagman.log" already exists.

Some file(s) needed by condor_dagman already exist. Either rename them,
use the "-f" option to force them to be overwritten, or use
the "-update_submit" option to update the submit file and continue.
ERROR: Running pegasus-submit-dag failed with exit code 1 at /usr/local/pegasus/bin/pegasus-run line 289.

I removed the files listed in the ERROR messages and everything seemed to work.

I tarred up the workflow and put it here: juve.isi.edu:/submit/kepler2012/work/gideon/pegasus/Run2-25/Run2-25.tar.gz