/groups/sbinlab/tiemann/dev/anaconda3/lib/python3.7/site-packages/Bio/SubsMat/__init__.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module.
  BiopythonDeprecationWarning,
usage: run_pipeline.py [-h] [--structure STRUC_FILE]
                       [--outputpath OUTPUT_FILE]
                       [--mode {print,create,proceed,fullrun,relax,ddg_calculation}]
                       [--mutate_mode {all,mut_file}]
                       [--mutations MUTATION_INPUT] [--chainid CHAIN]
                       [--run_struc RUN_STRUC] [--ligand LIGAND]
                       [--overwrite_path OVERWRITE_PATH]
                       [--slurm_partition SLURM_PARTITION]
                       [--gapped_output GAPS_OUTPUT] [--dump_pdb DUMP_PDB]
                       [--skip_zip ZIP_FILES] [--verbose VERBOSE]
                       [--is_membrane IS_MP] [--mp_span MP_SPAN_INPUT]
                       [--mp_calc_span_mode {False,struc,DSSP,octopus,bcl,Boctopus}]
                       [--mp_align_ref MP_ALIGN_REF]
                       [--mp_prep_align_mode {False,OPM,PDBTM,TMDET,MemProtMD}]
                       [--ddgflags DDG_FLAG_FILE]
                       [--relaxflags RELAX_FLAG_FILE]
                       [--mp_relax_xml RELAX_XML_INPUT]
run_pipeline.py: error: unrecognized arguments: --scale 1.0
current env paths & exec: /groups/sbinlab/software/TMalign/TMalign /groups/sbinlab/software/muscle/muscle3.8.31_i86linux64 /groups/sbinlab/software/PRISM_tools/rosetta_stability-v0.1.1/software/rosetta_ddG_pipeline /sbinlab/software/Rosetta_2021_Aug_c7009b3/source /groups/sbinlab/tiemann/dev/Rosetta/tools/ /sbinlab/software/Rosetta_2021_Aug_c7009b3/database default.linuxgccrelease /groups/sbinlab/software/PRISM_tools/prism_parser/scripts 3bd329948ac5de95a697cb9f1395929a6a557580 v0.1.1