error - maybe just because no input provided

[amelie-stein]

(base) [amelie@fend04 ddg_benchmark]$ run_ddG_pipeline_dev_amelie
/lustre/hpc/sbinlab/amelie/projects/PRISM/ddg_benchmark
Traceback (most recent call last):
File "/groups/sbinlab/amelie/projects/PRISM/PRISM/software/rosetta_ddG_pipeline/run_pipeline.py", line 148, in
predict_stability(sys.argv[1:])
File "/groups/sbinlab/amelie/projects/PRISM/PRISM/software/rosetta_ddG_pipeline/run_pipeline.py", line 71, in predict_stability
name = structure_list.split('/')[-1].split('.')[0]
UnboundLocalError: local variable 'structure_list' referenced before assignment

[j0kaso]

which branch are you working on?

[amelie-stein]

main branch

[amelie-stein]

another error, now on dev branch:
Traceback (most recent call last):
File "/groups/sbinlab/amelie/projects/PRISM/PRISM/software/rosetta_ddG_pipeline/run_pipeline.py", line 279, in
predict_stability(args)
File "/groups/sbinlab/amelie/projects/PRISM/PRISM/software/rosetta_ddG_pipeline/run_pipeline.py", line 68, in predict_stability
input_dict = storeinputs.storeinputfuc(name, args, folder)
File "/lustre/hpc/sbinlab/amelie/projects/PRISM/PRISM/software/rosetta_ddG_pipeline/storeinputs.py", line 38, in storeinputfuc
folder.input, basename(args.RELAX_FLAG_FILE)))
File "/groups/sbinlab/haagenb/anaconda3/lib/python3.7/shutil.py", line 120, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/groups/sbinlab/amelie/projects/PRISM/PRISM/software/rosetta_ddG_pipeline/#/rosetta_parameters/relax_flagfile'

[j0kaso]

how did you call the program? did you provide a relax_flagfile?
did you adapt the paths in your bashrc?

     'TMalign_exec': '/groups/sbinlab/software/TMalign/TMalign',
    'ddG_pipeline': '/sbinlab/software/PRISM/software/rosetta_ddG_pipeline',
    'Rosetta_main_path': '/sbinlab/software/Rosetta_2018_Oct_d557f8/source/',
    'Rosetta_tools_path': '/sbinlab/software/Rosetta_tools/tools/',
    'Rosetta_database_path': '/sbinlab/software/Rosetta_2018_Oct_d557f8/database/',
    'Rosetta_extension': 'linuxgccrelease',
    'prims_parser': '/sbinlab/tiemann/repos/PRISM/prism/scripts',