Error in Hybridize of Rosetta Comparative Modeling.

[Anonymous]

After threading my target fasta on template pdb, I ran Hybridyze rosetta_scripts. The terminal stopped in the error “Segmentation fault: 11”. I checked my command line and input files, and tried to find out what was going wrong, but I had no idea to find out what the problem was. All the tracebacks are listed below.

 

#

zpro:3-hybridize zzl$ /Users/zzl/rosetta_bin_mac_2019.22.60749_bundle/main/source/bin/rosetta_scripts.mpi.macosclangrelease @rosetta_cm.options

core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags 

core.init: (0) Rosetta version: rosetta.binary.mac.release-223 r223 2019.22+release.d8f9b4a90a8 d8f9b4a90a8f2caa32948bacdb6e551591facd5f https://www.rosettacommons.org 2019-05-31T19:16:11.723572

core.init: (0) command: /Users/zzl/rosetta_bin_mac_2019.22.60749_bundle/main/source/bin/rosetta_scripts.mpi.macosclangrelease @rosetta_cm.options

core.init: (0) ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1309188976 seed_offset=0 real_seed=1309188976

core.init.random: (0) RandomGenerator:init: Normal mode, seed=1309188976 RG_type=mt19937

core.init: (0) Resolved executable path: /Users/zzl/rosetta_bin_mac_2019.22.60749_bundle/main/source/bin/rosetta_scripts.mpi.macosclangrelease

core.init: (0) Looking for database based on location of executable: /Users/zzl/rosetta_bin_mac_2019.22.60749_bundle/main/database/

protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active … 

core.chemical.GlobalResidueTypeSet: (0) While generating GlobalResidueTypeSet centroid: Skipping patch VirtualBB as requested

core.chemical.GlobalResidueTypeSet: (0) While generating GlobalResidueTypeSet centroid: Skipping patch N_acetylated as requested

core.chemical.GlobalResidueTypeSet: (0) While generating GlobalResidueTypeSet centroid: Skipping patch C_methylamidated as requested

core.chemical.GlobalResidueTypeSet: (0) While generating GlobalResidueTypeSet centroid: Skipping patch ser_phosphorylated as requested

core.chemical.GlobalResidueTypeSet: (0) While generating GlobalResidueTypeSet centroid: Skipping patch thr_phosphorylated as requested

core.chemical.GlobalResidueTypeSet: (0) While generating GlobalResidueTypeSet centroid: Skipping patch ShoveBB as requested

core.chemical.GlobalResidueTypeSet: (0) While generating GlobalResidueTypeSet centroid: Skipping patch LowerDNA as requested

core.chemical.GlobalResidueTypeSet: (0) While generating GlobalResidueTypeSet centroid: Skipping patch UpperDNA as requested

core.chemical.GlobalResidueTypeSet: (0) While generating GlobalResidueTypeSet centroid: Skipping patch VirtualDNAPhosphate as requested

core.chemical.GlobalResidueTypeSet: (0) Finished initializing centroid residue type set.  Created 62 residue types

core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 0.052242 seconds.

[zpro:25945] *** Process received signal ***

[zpro:25945] Signal: Segmentation fault: 11 (11)

[zpro:25945] Signal code: Address not mapped (1)

[zpro:25945] Failing at address: 0x80

[zpro:25945] [ 0] 0   libsystem_platform.dylib            0x00007fff646abb5d _sigtramp + 29

[zpro:25945] [ 1] 0   ???                                 0x3fee2a1e7d02fe9e 0x0 + 4606665779281329822

[zpro:25945] [ 2] 0   libcore.2.dylib                     0x00000001112339be _ZN4core12conformation13carbohydrates28get_glycosidic_bond_residuesERKNS0_12ConformationEm + 574

[zpro:25945] [ 3] 0   libcore.2.dylib                     0x0000000111233bec _ZN4core12conformation13carbohydrates27get_reference_atoms_for_phiERKNS0_12ConformationEm + 60

[zpro:25945] [ 4] 0   libcore.2.dylib                     0x0000000111235053 _ZN4core12conformation13carbohydrates19get_reference_atomsEmRKNS0_12ConformationEm + 99

[zpro:25945] [ 5] 0   libcore.2.dylib                     0x0000000111237c69 _ZN4core12conformation13carbohydrates22set_glycosidic_torsionEmRNS0_12ConformationEmd + 41

[zpro:25945] [ 6] 0   libprotocols.3.dylib                0x000000010efdee7e _ZN9protocols5loops40set_extended_torsions_and_idealize_loopsERN4core4pose4PoseENS0_5LoopsE + 318

[zpro:25945] [ 7] 0   libprotocols.4.dylib                0x000000010e17978d _ZN9protocols13pose_creation17ExtendedPoseMover5applyERN4core4pose4PoseE + 109

[zpro:25945] [ 8] 0   libprotocols_g.5.dylib              0x000000010cf7f769 _ZN9protocols20comparative_modeling18GenericJobInputter13pose_from_jobERN4core4pose4PoseENSt3__110shared_ptrINS_3jd23JobEEE + 1257

[zpro:25945] [ 9] 0   libprotocols.1.dylib                0x000000010fe3ce37 _ZN9protocols3jd214JobDistributor11run_one_jobERNSt3__110shared_ptrINS_5moves5MoverEEElRNS2_12basic_stringIcNS2_11char_traitsIcEENS2_9allocatorIcEEEESE_RmSF_b + 2983

[zpro:25945] [10] 0   libprotocols.1.dylib                0x000000010fe3b5d3 _ZN9protocols3jd214JobDistributor7go_mainENSt3__110shared_ptrINS_5moves5MoverEEE + 195

[zpro:25945] [11] 0   libprotocols.1.dylib                0x000000010fe35db6 _ZN9protocols3jd224FileSystemJobDistributor2goENSt3__110shared_ptrINS_5moves5MoverEEE + 70

[zpro:25945] [12] 0   rosetta_scripts.mpi.macosclangrelease 0x000000010a10c806 main + 1206

[zpro:25945] [13] 0   libdyld.dylib                       0x00007fff644c03d5 start + 1

 

#Thanks for helping!

[Anonymous]

It looks like it’s having issues in the carbohydrate subsystem.

Are you modeling a system with any carbohydrate residues or glycosides? Are there any non-canonical residues in your protein (anything besides the standard 20)?

[Author]

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