In one of the examples, we get the stage job to fail removing the input file
pegtrain01@workflow:~/examples/split/pegtrain01/pegasus/split/run0002$ cat stage_in_remote_local_0_0.in

1. src 1 local prio 0
   file:///nfs/ccg3/ccg/home/pegtrain01/examples/split/input/pegasus.html
2. dst 1 local
   file:///nfs/ccg3/ccg/home/pegtrain01/run/pegtrain01/pegasus/split/run0002/pegasus.html
   pegtrain01@workflow:~/examples/split/pegtrain01/pegasus/split/run0002$

The transfer job runs locally.

pegtrain01@workflow:~/examples/split/pegtrain01/pegasus/split/run0002$ time pegasus-transfer -n 1 -f stage_in_remote_local_0_0.in
2015-10-23 15:19:55,917 INFO: Reading URL pairs from stage_in_remote_local_0_0.in
2015-10-23 15:19:55,917 INFO: PATH=/usr/bin:/usr/local/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin
2015-10-23 15:19:55,917 INFO: LD_LIBRARY_PATH=
2015-10-23 15:19:55,918 INFO: 1 transfers loaded
2015-10-23 15:19:55,919 INFO: Sorting the tranfers based on transfer type and source/destination
2015-10-23 15:19:55,919 INFO: --------------------------------------------------------------------------------
2015-10-23 15:19:55,919 INFO: Starting transfers - attempt 1
2015-10-23 15:19:55,919 INFO: Using 1 threads for this round of transfers
/bin/cp: cannot stat `/nfs/ccg3/ccg/home/pegtrain01/examples/split/input/pegasus.html': No such file or directory
2015-10-23 15:19:57,929 ERROR: Command exited with non-zero exit code (1): /bin/cp -f -R -L '/nfs/ccg3/ccg/home/pegtrain01/examples/split/input/pegasus.html' '/nfs/ccg3/ccg/home/pegtrain01/run/pegtrain01/pegasus/split/run0002/pegasus.html'
2015-10-23 15:20:33,966 INFO: --------------------------------------------------------------------------------
2015-10-23 15:20:33,966 INFO: Starting transfers - attempt 2
2015-10-23 15:20:33,966 INFO: Using 1 threads for this round of transfers
/bin/cp: cannot stat `/nfs/ccg3/ccg/home/pegtrain01/examples/split/input/pegasus.html': No such file or directory
2015-10-23 15:20:35,977 ERROR: Command exited with non-zero exit code (1): /bin/cp -f -R -L '/nfs/ccg3/ccg/home/pegtrain01/examples/split/input/pegasus.html' '/nfs/ccg3/ccg/home/pegtrain01/run/pegtrain01/pegasus/split/run0002/pegasus.html'
2015-10-23 15:23:36,078 INFO: --------------------------------------------------------------------------------
2015-10-23 15:23:36,078 INFO: Starting transfers - attempt 3
2015-10-23 15:23:36,079 INFO: Using 1 threads for this round of transfers
/bin/cp: cannot stat `/nfs/ccg3/ccg/home/pegtrain01/examples/split/input/pegasus.html': No such file or directory
2015-10-23 15:23:38,091 ERROR: Command exited with non-zero exit code (1): /bin/cp -f -R -L '/nfs/ccg3/ccg/home/pegtrain01/examples/split/input/pegasus.html' '/nfs/ccg3/ccg/home/pegtrain01/run/pegtrain01/pegasus/split/run0002/pegasus.html'
2015-10-23 15:23:38,091 INFO: --------------------------------------------------------------------------------
2015-10-23 15:23:38,091 INFO: Stats: no local files in the transfer set
2015-10-23 15:23:38,092 CRITICAL: Some transfers failed! See above, and possibly stderr.

real 3m42.258s
user 0m0.085s
sys 0m0.022s

Looking at the output it appears, there is a delay of one minute before pegasus-transfer starts the retry.

is this deliberate?