Branch: rosetta:commits 「revision: №20727」
Test: ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit
SubTest: T009_Exceptions
SubTest files: 「file-system-view」
Daemon: nobu-3    
State: T009_Exceptions

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2025.12.post.dev+366.HEAD.eb335bbef6 eb335bbef6d6c316ce39cc03c8dca6ea8f2c8ac3 git@github.com:RosettaCommons/rosetta.git 2025-04-03T17:18:52 core.init: Rosetta extras: [cxx11thread, serialization] core.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/build/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=2108136310 seed_offset=0 real_seed=2108136310 thread_index=0 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=2108136310 RG_type=mt19937 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.57384 seconds. basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb basic.io.database: Database file op┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2025 [Rosetta devel 2025.12.post.dev+366.HEAD.eb335bbef6d6c316ce39cc03c8dca6ea8f2c8ac3 2025-04-03T17:18:52] retrieved from: git@github.com:RosettaCommons/rosetta.git Exceptions type: <class 'RuntimeError'>, message: File: /home/benchmark/rosetta/source/src/protocols/rosetta_scripts/RosettaScriptsParser.cc:514 parser::protocol file must specify PROTOCOLS section ened: scoring/score_functions/rama/flat/avg_L_rama.dat core.scoring.ramachandran: Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama.dat. basic.io.database: Database file opened: scoring/score_functions/rama/flat/sym_all_rama.dat core.scoring.ramachandran: Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama.dat. basic.io.database: Database file opened: scoring/score_functions/rama/flat/sym_G_rama.dat core.scoring.ramachandran: Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama.dat. basic.io.database: Database file opened: scoring/score_functions/rama/flat/sym_P_rama.dat core.scoring.ramachandran: Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama.dat. basic.io.database: Database file opened: scoring/score_functions/rama/flat/avg_L_rama_str.dat core.scoring.ramachandran: Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama_str.dat. basic.io.database: Database file opened: scoring/score_functions/rama/flat/sym_all_rama_str.dat core.scoring.ramachandran: Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama_str.dat. basic.io.database: Database file opened: scoring/score_functions/rama/flat/sym_G_rama_str.dat core.scoring.ramachandran: Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama_str.dat. basic.io.database: Database file opened: scoring/score_functions/rama/flat/sym_P_rama_str.dat core.scoring.ramachandran: Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama_str.dat. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 Finished T009_Exceptions in 0:00:14.549901