Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › Segmentation Fault
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AuthorPosts
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March 29, 2019 at 6:21 pm #3102
Anonymous
Hi,
I am trying to use protein-protein docking with unbound ligand protein and, I still get this error(see below ). I would appreciate any suggestion or solution.
Looking forward to hearing from you.
Haresh
hajani@sgc-titan:~/Lab/Projects/p3_Rosetta$ ../../../Software/rosetta_2019/main/source/bin/docking_protocol.static.linuxgccrelease @flag_local_docking
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.linux.release-215 r215 2019.12+release.46f270e 46f270eaa6df591e0db5e65cdd09b31ec37b7d41 https://www.rosettacommons.org 2019-03-26T05:33:04.958196
core.init: command: ../../../Software/rosetta_2019/main/source/bin/docking_protocol.static.linuxgccrelease @flag_local_docking
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1979622128 seed_offset=0 real_seed=-1979622128
core.init.random: RandomGenerator:init: Normal mode, seed=-1979622128 RG_type=mt19937
core.init: Resolved executable path: /home/disk0/hajani/Software/rosetta_2019/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/docking_protocol.static.linuxgccrelease
core.init: Looking for database based on location of executable: /home/disk0/hajani/Software/rosetta_2019/main/database/
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.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 696 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.64 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.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.docking.DockingInitialPerturbation: Reading options…
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input_files/col_complex1.pdb nstruct indices 1 – 50
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input_files/col_complex1.pdb
core.import_pose.import_pose: File ‘input_files/col_complex1.pdb’ automatically determined to be of type PDB
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 1 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG2 in residue 1 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 3 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 3 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 3 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 18 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 18 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 18 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 18 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 107 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 107 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 113 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 113 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 113 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 113 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 113 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 125 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 125 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 125 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE2 in residue 125 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 131 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 131 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 131 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 131 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 132 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 132 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 132 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 132 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.chemical.GlobalResidueTypeSet: Loading ‘CAS’ from the PDB components dictionary for residue type ‘pdb_CAS’
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue MET:CtermProteinFull 108
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL:NtermProteinFull 109
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue VAL:NtermProteinFull 109
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 111
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 111
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 111
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 126
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 126
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 126
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 126
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 215
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 215
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 221
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 221
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 221
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 221
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 221
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 233
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 233
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 233
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 233
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 239
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 239
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 239
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 239
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 240
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 240
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 240
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 240
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 246
core.pack.pack_missing_sidechains: packing residue number 109 because of missing atom number 6 atom name CG1
core.pack.pack_missing_sidechains: packing residue number 111 because of missing atom number 9 atom name CZ
core.pack.pack_missing_sidechains: packing residue number 126 because of missing atom number 8 atom name NE
core.pack.pack_missing_sidechains: packing residue number 215 because of missing atom number 8 atom name CE
core.pack.pack_missing_sidechains: packing residue number 221 because of missing atom number 7 atom name CD
core.pack.pack_missing_sidechains: packing residue number 226 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 240 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 244 because of missing atom number 6 atom name CG
core.pack.task: Packer task: initialize from command line()
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/disk0/hajani/Software/rosetta_2019/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file ‘/home/disk0/hajani/Software/rosetta_2019/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin’.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.12 seconds to load from binary
core.pack.pack_rotamers: built 102 rotamers at 10 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.docking.DockingInitialPerturbation: Reading options…
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.docking.DockingProtocol: Danger Will Robinson! Native is an impostor!
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 108 -1 EDGE 1 109 1 EDGE 109 246 -1
protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 76 -1 EDGE 76 108 -1 EDGE 76 167 1 EDGE 167 109 -1 EDGE 167 246 -1
Segmentation fault (core dumped)
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March 29, 2019 at 6:42 pm #14626
(Copying from another answer about segfaults I just wrote)
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April 2, 2019 at 1:50 pm #14639
Thanks Rmoretti for your reply. I have tried with debug mode. I still get error(see below). Please let me know what is exact probelm?
Haresh
hajani@sgc-titan:~/Lab/Projects/p3_Rosetta$ ../../../Software/rosetta_2019/main/source/bin/docking_protocol.linuxgccdebug @flag_local_docking
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.linux.release-215 r215 2019.12+release.46f270e 46f270eaa6df591e0db5e65cdd09b31ec37b7d41 https://www.rosettacommons.org 2019-03-26T05:33:04.958196
core.init: command: ../../../Software/rosetta_2019/main/source/bin/docking_protocol.linuxgccdebug @flag_local_docking
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1192988435 seed_offset=0 real_seed=1192988435
core.init.random: RandomGenerator:init: Normal mode, seed=1192988435 RG_type=mt19937
core.init: Resolved executable path: /home/disk0/hajani/Software/rosetta_2019/main/source/build/src/debug/linux/4.15/64/x86/gcc/7/default/docking_protocol.default.linuxgccdebug
core.init: Looking for database based on location of executable: /home/disk0/hajani/Software/rosetta_2019/main/database/
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.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 696 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 16.5056 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.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.docking.DockingInitialPerturbation: Reading options…
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input_files/col_complex1.pdb nstruct indices 1 – 50
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input_files/col_complex1.pdb
core.import_pose.import_pose: File ‘input_files/col_complex1.pdb’ automatically determined to be of type PDB
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 1 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG2 in residue 1 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 3 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 3 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 3 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 18 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 18 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 18 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 18 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 107 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 107 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 113 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 113 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 113 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 113 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 113 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 118 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 125 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 125 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 125 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE2 in residue 125 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 131 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 131 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 131 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 131 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 132 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 132 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 132 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 132 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 136 C. Pass flag -ignore_zero_occupancy false to change this behavior
core.chemical.GlobalResidueTypeSet: Loading ‘CAS’ from the PDB components dictionary for residue type ‘pdb_CAS’
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue MET:CtermProteinFull 108
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL:NtermProteinFull 109
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue VAL:NtermProteinFull 109
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 111
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 111
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 111
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 126
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 126
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 126
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 126
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 215
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 215
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 221
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 221
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 221
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 221
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 221
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 226
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 233
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 233
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 233
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 233
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 239
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 239
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 239
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 239
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 240
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 240
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 240
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 240
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 244
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 246
core.pack.pack_missing_sidechains: packing residue number 109 because of missing atom number 6 atom name CG1
core.pack.pack_missing_sidechains: packing residue number 111 because of missing atom number 9 atom name CZ
core.pack.pack_missing_sidechains: packing residue number 126 because of missing atom number 8 atom name NE
core.pack.pack_missing_sidechains: packing residue number 215 because of missing atom number 8 atom name CE
core.pack.pack_missing_sidechains: packing residue number 221 because of missing atom number 7 atom name CD
core.pack.pack_missing_sidechains: packing residue number 226 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 240 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 244 because of missing atom number 6 atom name CG
core.pack.task: Packer task: initialize from command line()
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/disk0/hajani/Software/rosetta_2019/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file ‘/home/disk0/hajani/Software/rosetta_2019/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin’.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.756061 seconds to load from binary
core.pack.pack_rotamers: built 102 rotamers at 10 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: VRRKRREQKR, best_energy: -4.1211
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.docking.DockingInitialPerturbation: Reading options…
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.docking.DockingProtocol: Danger Will Robinson! Native is an impostor!
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 108 -1 EDGE 1 109 1 EDGE 109 246 -1
protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 76 -1 EDGE 76 108 -1 EDGE 76 167 1 EDGE 167 109 -1 EDGE 167 246 -1
/usr/include/c++/7/debug/safe_iterator.h:270:
Error: attempt to dereference a past-the-end iterator.
Objects involved in the operation:
iterator “this” @ 0x0x7ffcbb9a27f0 {
type = __gnu_debug::_Safe_iterator<__gnu_cxx::__normal_iterator<unsigned long*, std::__cxx1998::vector<unsigned long, std::allocator<unsigned long> > >, std::__debug::vector<unsigned long, std::allocator<unsigned long> > > (mutable iterator);
state = past-the-end;
references sequence with type ‘std::__debug::vector<unsigned long, std::allocator<unsigned long> >’ @ 0x0x7ffcbb9a28d8
}
Got some signal… It is:6
Process was aborted!
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April 3, 2019 at 4:19 pm #14642
I’m not seeing anything that’s immediately helpful in helping to identify the cause of the issue. The “attempt to dereference a past-the-end iterator.” is telling me that the issue is probably related to a size mismatch – one thing is telling Rosetta there’s X many things, and another is telling it there’s Y things. Undortunately, there isn’t much info on where those differences are coming from, or what the true size should be.
One thing to do, if you haven’t already, is try to minimize/simplify your protocol. If you progressively make things simpler, there may be a point where you see the error disappear, and that will point to where the issue might be coming from.
If that doesn’t help, the next thing to try is to run under conditions which will give you a backtrace. Sometimes running with the `catchsegv` application (just prepend `catchsegv` before the command will help there, or otherwise you may need to run under a debugger and get a backtrace there.
If you can’t get that to work on your end, you can bundle together all the input files needed to get things to run, and post them (or a link to them) here, and someone on our side can try reproducing the crash locally.
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April 4, 2019 at 2:07 pm #14647
Thanks rmoretti for your reply. Please find the attached files as you requested.
Following, I used docking input “flag_local_docking”
-in:file:s input_files/col_complex.pdb
-unboundrot input_files/col_complex.pdb
-nstruct 50
-partners A_B
-dock_pert 3 8
-ex1
-ex2aro
-out:path:all output_files
-out:suffix _local_dock
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AuthorPosts
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Segmentation faults are difficult to debug, in part because of the limited amount of information that is availible. (But you can take scant solace in the fact that segfaults are totally the fault of Rosetta developers – at the very least we should be providing you an error message, rather than a segfault.)
The first step in debugging a segfault is to double-check all your inputs. Segfaults are normally caused by conditions which the programmer didn’t anticipate. If there’s something “off” about your inputs – if there’s formatting issues, or you’re not matching the way the program expects things to be formatted – that can often be the cause of the segfault.
The next step, if there’s nothing obviously wrong with the inputs, is to compile the debug mode of Rosetta (add “mode=debug” to the scons command line, rather than “mode=release”, and use the “docking_protocol.static.linuxgccdebug” executable rather than “docking_protocol.static.linuxgccdebug” one). This has extra checking which slows the run down, but can give you better diagnostics. Often this can give a better indication of what went wrong.
If that doesn’t help, you may need to run things under a debugger to get a backtrace of where the segfault is happening.
Feel free to post what additional information you have here. If you can bundle up enough of your inputs such that we can try the run on our own machines, that can sometimes help. It’s not always easy to see what might be going on without a better understanding of Rosetta internals.