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

*********************************************************************************************************************************************************************************

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: 

---

           

---

 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 %sn(usually added by <method>/options.py during setup)”%(file,self.name))