core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.mac.release-280 r280 2021.16+release.8ee4f02ac57 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T11:45:16.822269 core.init: command: /Users/ncohen/Desktop/rosetta/main/source/bin//trRosetta.tensorflow.macosclangdebug @rosetta-2.flags basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1496890560 seed_offset=0 real_seed=1496890560 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1496890560 RG_type=mt19937 core.init: Resolved executable path: /Users/ncohen/Desktop/rosetta/main/source/bin//trRosetta.tensorflow.macosclangdebug core.init: Looking for database based on location of executable: /Users/ncohen/Desktop/rosetta/main/database/ apps.public.trRosetta.trRosetta: Starting trRosetta application. apps.public.trRosetta.trRosetta: Application created 21 January 2021 by Vikram K. Mulligan, Flatiron Institute (vmulligan@flatironinstitute.org). apps.public.trRosetta.trRosetta: Original trRosetta neural network developed by Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, and David Baker. (https://doi.org/10.1073/pnas.1914677117). protocols.trRosetta_protocols.movers.trRosettaProtocolMover: No native structure specified. Not setting native structure in trRosettaProtocol mover. basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_hb_params.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 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 core.energy_methods.CenHBEnergy: Configured CenHBEnergy to use soft potential based on locally-set options. protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Set scorefunction for centroid stage 0 to trRosetta_cen0.wts. core.energy_methods.CenHBEnergy: Configured CenHBEnergy to use soft potential based on locally-set options. protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Set scorefunction for centroid stage 1 to trRosetta_cen1.wts. protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Set scorefunction for centroid stage 2 to trRosetta_cen2.wts. 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.energy_methods.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 80 , 10 , 80 basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt core.energy_methods.CartesianBondedEnergy: Read 759 bb-independent lengths. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt core.energy_methods.CartesianBondedEnergy: Read 1434 bb-independent angles. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt core.energy_methods.CartesianBondedEnergy: Read 1 bb-independent torsions. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt core.energy_methods.CartesianBondedEnergy: Read 529 bb-independent improper tors. protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Set scorefunction for centroid stage 3 to trRosetta_cart.wts. 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. core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 7.8739 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/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 protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Set scorefunction for full-atom refinement to ref2015. protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Setting full-atom refinement scorefunction atom_pair_constraint weight to 5.0 (was 0.0). protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Setting full-atom refinement scorefunction dihedral_constraint weight to 1.0 (was 0.0). protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Setting full-atom refinement scorefunction angle_constraint weight to 1.0 (was 0.0). protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.15917 seconds. protocols.relax.RelaxScriptManager: Reading relax scripts list from database. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt protocols.relax.RelaxScriptManager: ================== Reading script file: /Users/ncohen/Desktop/rosetta/main/database/sampling/relax_scripts/MonomerRelax2019.txt ================== protocols.relax.RelaxScriptManager: repeat %%nrepeats%% protocols.relax.RelaxScriptManager: coord_cst_weight 1.0 protocols.relax.RelaxScriptManager: scale:fa_rep 0.040 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.051 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.5 protocols.relax.RelaxScriptManager: scale:fa_rep 0.265 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.280 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.0 protocols.relax.RelaxScriptManager: scale:fa_rep 0.559 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.581 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.0 protocols.relax.RelaxScriptManager: scale:fa_rep 1 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: min 0.00001 protocols.relax.RelaxScriptManager: accept_to_best protocols.relax.RelaxScriptManager: endrepeat protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Starting trRosetta structure prediction protocol. protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Building pose from sequence. protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Randomizing backbone dihedrals using protocol "ramachandran". protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Removing clashes. protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Initializing constraint generator from multiple sequence alignment file "r10-old.a3m". protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator: Configuring trRosettaConstraintGenerator to set distance constraints. protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator: Configuring trRosettaConstraintGenerator to set omega dihedral constraints. protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator: Configuring trRosettaConstraintGenerator to set theta dihedral constraints. protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator: Configuring trRosettaConstraintGenerator to set phi angle constraints. protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator: Configuring trRosettaConstraintGenerator to set distance constraints. protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator: Configuring trRosettaConstraintGenerator to set omega dihedral constraints. protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator: Configuring trRosettaConstraintGenerator to set theta dihedral constraints. protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator: Configuring trRosettaConstraintGenerator to set phi angle constraints. protocols.trRosetta_protocols.movers.trRosettaProtocolMover: Generating trRosetta constraints. protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator: Loading trRosetta model version 1. 2021-05-04 12:08:48.787167: I tensorflow/cc/saved_model/reader.cc:31] Reading SavedModel from: /Users/ncohen/Desktop/rosetta/main/database/protocol_data/tensorflow_graphs/tensorflow_graph_repo_submodule/trRosetta/model_v1/ 2021-05-04 12:08:48.951722: I tensorflow/cc/saved_model/reader.cc:54] Reading meta graph with tags { serve } 2021-05-04 12:08:49.140970: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2021-05-04 12:08:49.166025: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7ff7f6e4a9c0 initialized for platform Host (this does not guarantee that XLA will be used). Devices: 2021-05-04 12:08:49.166099: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version 2021-05-04 12:08:49.686583: I tensorflow/cc/saved_model/loader.cc:202] Restoring SavedModel bundle. 2021-05-04 12:08:49.686690: I tensorflow/cc/saved_model/loader.cc:212] The specified SavedModel has no variables; no checkpoints were restored. File does not exist: /Users/ncohen/Desktop/rosetta/main/database/protocol_data/tensorflow_graphs/tensorflow_graph_repo_submodule/trRosetta/model_v1/variables/variables.index 2021-05-04 12:08:49.686716: I tensorflow/cc/saved_model/loader.cc:311] SavedModel load for tags { serve }; Status: success. Took 899561 microseconds. ERROR: Assertion `coord1 > 0 && coord1 <= static_cast( TF_Dim(tensor_, 0) )` failed. ERROR:: Exit from: src/basic/tensorflow_manager/RosettaTensorflowTensorContainer.hh line: 254 AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. Assertion failed: (( coord1 > 0 && coord1 <= static_cast( TF_Dim(tensor_, 0) ) ) || handle_assert_failure( "coord1 > 0 && coord1 <= static_cast( TF_Dim(tensor_, 0) )", __FILE__, __LINE__ )), function operator(), file src/basic/tensorflow_manager/RosettaTensorflowTensorContainer.hh, line 254. Got some signal... It is:6 Signal 6 (SIGABRT) means that the process was aborted. This usually means an internal Rosetta error caused by (often) bad inputs, (sometimes) developer error, or (rarely) hardware problems. basic.tensorflow_manager.RosettaTensorflowManager: [ ERROR ] Error in RosettaTensorflowManager destructor: The Tensorflow session indexed with <"protocol_data/tensorflow_graphs/tensorflow_graph_repo_submodule/trRosetta/model_v1/", "serve", 0x0> is in use by 1 other users! s!