setup_run error with multiple resonance lists

Hello.

I'm trying to set up an autoNOE protocol specifying an assigned resonance list for each peak list in setup_target. However, when I do this, setup_autoNOE.py fails with the error listed below. I tried generating just one run directory with setup_run.py -traceback and have copied the error stack trace. When I specify a single .prot resonance list, it works just fine, but when I specify multiple files it gives these errors. The files are copied just fine in /nmr_data during the setup_target.py step, so they are there even though the error says they cannot be found. I need to be able to specify an assigned list for each noesy peak list. I can set up each run directory and flag file by hand if necessary, but I can't find an example of what these are supposed to look like when multiple resonance lists are specified. Can anyone help me either solve this error or provide an example of setup/flag files when multiple .prot lists are specified? 

Thank you!

setup_autoNOE -target test -method autoNOE -dir ../cs_targetlib/ -job moab -extras mpi
['-target', 'test', '-method', 'autoNOE', '-dir', '../cs_targetlib/', '-job', 'moab', '-extras', 'mpi']
*********************************************************************************************************************************************************************************
EXECUTE META SCRIPT: setup_run -method autoNOE -run_label cst_05 -noesy_cst_strength 5 -target test -method autoNOE -dir ../cs_targetlib/ -job moab -extras mpi
*********************************************************************************************************************************************************************************
integrate job: interactive from library
integrate job: moab from library
integrate job: slurm from library
Build job-files  moab
mpi.linuxgccrelease

Setup( test | autoNOE_standard )

============================================================
LOADED: Method options from existing setup 'autoNOE_standard'...
- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -
Method: autoNOE
Chosen Options: 
   cs nmr_data/t000.tab
   fasta fragments/t000.fasta
   frags fragments/t000.frags3.dat.gz fragments/t000.frags9.dat.gz
   no_auto_intensities False
   peaks nmr_data/n.peaks nmr_data/ali.peaks nmr_data/aro.peaks
   shifts nmr_data/n.trim.prot nmr_data/ali.trim.prot nmr_data/aro.trim.prot
------------------------------------------------------------

replacing the restraint strenght with cmd-line controlled weight...
generate run from  Setup( test | autoNOE_standard )
CM_DIR:  /home/user/cs_targetlib/test
inputs/flags_autoNOE
RunGenerator: generate targetflags inputs/flags_autoNOE as ../cs_targetlib/test/cst_05/inputs/flags_autoNOE
prepare prot files for autoNOE-Rosetta ...
ProgramError: 

------------------      ['cannot find file $CM_TARGETPATH/nmr_data/n.trim.prot in Target test\n(usually added by <method>/options.py during setup)']      --------------------------------------------

 please send a description of what you were doing, the cmd-line and the stack-trace (run with -traceback) to
 to : oliver.lange@tum.de 

None
Error occurred in command "setup_run -method autoNOE -run_label cst_05 -noesy_cst_strength 5 -target test -method autoNOE -dir ../cs_targetlib/ -job moab -extras mpi"

# This is the traceback stack-trace:

inputs/flags_autoNOE
RunGenerator: generate targetflags inputs/flags_autoNOE as ../../cs_targetlib/test/cst_05/inputs/flags_autoNOE
prepare prot files for autoNOE-Rosetta ...
Traceback (most recent call last):
  File "/opt/rosetta/3/csrosetta3/com_alias/setup_run", line 163, in <module>
    my_run.generate_flags( setup, application.method )
  File "/opt/rosetta/3/csrosetta3/python/automatic_setup/RunGenerator.py", line 178, in generate_flags
    self.setup_target_flags( method, setup )
  File "/opt/rosetta/3/csrosetta3/python/automatic_setup/RunGenerator.py", line 113, in setup_target_flags
    method.make_target_flags(self, setup, self.targetflags, flag_file, self.SUBS )
  File "/opt/rosetta/3/csrosetta3/flag_library/methods/autoNOE/options.py", line 171, in make_target_flags
    prots=self.prepare_prot( setup, prots )
  File "/opt/rosetta/3/csrosetta3/flag_library/methods/autoNOE/options.py", line 114, in prepare_prot
    tr.out("will go %s --> %s"%(setup.abspath(input_shifts), setup.abspath(prot)))
  File "/opt/rosetta/3/csrosetta3/python/automatic_setup/Setup.py", line 151, in abspath
    return self.target.abspath(file,subdir=subdir)
  File "/opt/rosetta/3/csrosetta3/python/automatic_setup/TargetDir.py", line 220, in abspath
    self.raise_missing_file_error( file )
  File "/opt/rosetta/3/csrosetta3/python/automatic_setup/TargetDir.py", line 320, in raise_missing_file_error
    raise library.ProgramError("cannot find file %s in Target %s\n(usually added by <method>/options.py during setup)"%(file,self.name))