A forgotten System.out.println means a lot of extra debugging output:

$ pegasus-plan --conf ~/etc/pegasus.conf --sites condor_pool --output-site local --dax dag.xml
Create dir site for job stage_in_local_local_0_1 is local
Create dir site for job stage_in_local_local_0_0 is local
Create dir site for job stage_in_local_local_0_3 is local
Create dir site for job stage_in_local_local_0_2 is local
Create dir site for job stage_in_local_local_2_0 is local
Create dir site for job stage_in_local_local_3_0 is local
Create dir site for job stage_in_local_local_6_0 is local
Create dir site for job stage_in_local_local_5_0 is local
Create dir site for job mProjectPP_ID000008 is local
Create dir site for job mProjectPP_ID000006 is local
Create dir site for job mProjectPP_ID000005 is local
Create dir site for job mProjectPP_ID000002 is local
Create dir site for job mProjectPP_ID000004 is local
Create dir site for job mProjectPP_ID000001 is local
Create dir site for job mProjectPP_ID000007 is local
Create dir site for job mProjectPP_ID000003 is local
Create dir site for job mDiffFit_ID000021 is local
Create dir site for job mDiffFit_ID000018 is local
Create dir site for job mDiffFit_ID000020 is local
Create dir site for job mDiffFit_ID000015 is local
Create dir site for job mDiffFit_ID000017 is local
Create dir site for job mDiffFit_ID000009 is local
Create dir site for job mDiffFit_ID000010 is local
Create dir site for job mDiffFit_ID000012 is local
Create dir site for job mDiffFit_ID000016 is local
Create dir site for job mDiffFit_ID000019 is local
Create dir site for job mDiffFit_ID000011 is local
Create dir site for job mDiffFit_ID000013 is local
Create dir site for job mDiffFit_ID000014 is local
Create dir site for job mConcatFit_ID000022 is local
Create dir site for job mBgModel_ID000023 is local
Create dir site for job mBackground_ID000024 is local
Create dir site for job mBackground_ID000025 is local
Create dir site for job mBackground_ID000026 is local
Create dir site for job mBackground_ID000027 is local
Create dir site for job mBackground_ID000028 is local
Create dir site for job mBackground_ID000029 is local
Create dir site for job mBackground_ID000030 is local
Create dir site for job mBackground_ID000031 is local
Create dir site for job mImgtbl_ID000032 is local
Create dir site for job mAdd_ID000033 is local
Create dir site for job mShrink_ID000034 is local
Create dir site for job stage_out_remote_local_6_0 is local
Create dir site for job mJPEG_ID000035 is local
Create dir site for job stage_out_remote_local_7_0 is local
Create dir site for job stage_out_remote_local_8_0 is local
2013.10.27 04:32:52.529 UTC:

I have concretized your abstract workflow. The workflow has been entered
into the workflow database with a state of "planned". The next step is
to start or execute your workflow. The invocation required is

pegasus-run /home/montage/montage-workflow/montage/pegasus/montage/run0001

This can also be seen all over our Bamboo tests.