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ERROR: Assertion `static_cast< size_type >( i - l_ ) < super::size()` failed. ERROR:: Exit from: src/utility/vectorL.hh line: 42

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ERROR: Assertion `static_cast< size_type >( i - l_ ) < super::size()` failed. ERROR:: Exit from: src/utility/vectorL.hh line: 42
#1

Hi,

I'm trying to generate model from CM. There is error message shown as the topic (as uploaded crash file).

'Singal 6' is given at stage 4:

Stage 4                                                         
   Folding with score3 for 400
protocols.hybridization.FoldTreeHybridize: Stage 4 loop iteration 1: small fragments trials
protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 12842.1 12840.2
protocols.moves.TrialCounter:  ChunkTrialMover trials=     71;  accepts= 0.2817;  energy_drop/trial=  -0.07202
protocols.moves.TrialCounter: WeightedFragment trials=    329;  accepts= 0.1429;  energy_drop/trial=  -0.00831
protocols.hybridization.FoldTreeHybridize: Stage 4 loop iteration 2: small fragments smooth trials
protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 12836.1 12836
protocols.moves.TrialCounter:  ChunkTrialMover trials=     58;  accepts= 0.3793;  energy_drop/trial=  -0.20068
protocols.moves.TrialCounter: WeightedFragment trials=    342;  accepts= 0.1930;  energy_drop/trial=   0.01623
protocols.hybridization.FoldTreeHybridize: Stage 4 loop iteration 3: small fragments smooth trials
protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 12846.2 12835.8
protocols.moves.TrialCounter:  ChunkTrialMover trials=     70;  accepts= 0.3857;  energy_drop/trial=   0.02423
protocols.moves.TrialCounter: WeightedFragment trials=    330;  accepts= 0.1303;  energy_drop/trial=   0.02201
core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 1
core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 27 to 1
protocols.hybridization.HybridizeProtocol: Realigning template domains to stage1 pose.
core.util.switchresiduetypeset: [ WARNING ] When switching to a centroid ResidueTypeSet:  Pose already contains centroid ResidueTypes.
protocols.hybridization.CartesianHybridize: RUNNING FOR 4 MACROCYCLES
protocols.hybridization.CartesianHybridize:  total_res=489   prot_res=489
protocols.hybridization.CartesianHybridize: CYCLE 1
protocols.hybridization.CartesianHybridize:   setting bonded weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded angle weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded length weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded torsion weight = 0
protocols.hybridization.CartesianHybridize:   setting cst    weight = 0.5
protocols.hybridization.CartesianHybridize:   setting vdw    weight = 0.1
core.energy_methods.CartesianBondedEnergy: Creating new peptide-bonded energy container (489)
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: CA,N,H to DB with theta0 = 2.07956 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: N,CA,C to DB with theta0 = 1.94081 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: N,CA,CB to DB with theta0 = 1.92861 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: N,CA,CEN to DB with theta0 = 1.9856 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: C,CA,CB to DB with theta0 = 1.92174 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: C,CA,CEN to DB with theta0 = 2.12444 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: CB,CA,CEN to DB with theta0 = 0.317107 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: CA,C,O to DB with theta0 = 2.0944 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: N,CA, to DB with d0 = 1.458 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: N,H, to DB with d0 = 1.01 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: CA,C, to DB with d0 = 1.52326 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: CA,CB, to DB with d0 = 1.52951 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: CA,CEN, to DB with d0 = 3.51447 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: C,O, to DB with d0 = 1.2 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: C,N,CA to DB with theta0 = 2.12407 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: CB,CA,C to DB with theta0 = 1.92174 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: CA,N,C to DB with theta0 = 2.12407 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: H,N,C to DB with theta0 = 2.07956 , Ktheta = 80
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.

May I know how to further diagnose the problem and fix it? Thanks,

Yu

AttachmentSize
ROSETTA_CRASH.log88.5 KB
Post Situation: 
Wed, 2022-06-15 22:22
yliang20

Hi Yu,

May I know if you have find any solution to this error?

I also facing similar problem when running rosettaCM.

Same crashes at stage 4,

======================================================================================================================================
   Stage 4                                                         
   Folding with score3 for 400
protocols.hybridization.FoldTreeHybridize: Stage 4 loop iteration 1: small fragments trials
protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 7159.45 7159.45
protocols.moves.TrialCounter:  ChunkTrialMover trials=      8;  accepts= 0.3750;  energy_drop/trial=  -0.02618
protocols.moves.TrialCounter: WeightedFragment trials=    392;  accepts= 0.0357;  energy_drop/trial=  -0.11127
protocols.hybridization.FoldTreeHybridize: Stage 4 loop iteration 2: small fragments smooth trials
protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 7199 7195.43
protocols.moves.TrialCounter:  ChunkTrialMover trials=      1;  accepts= 1.0000;  energy_drop/trial=   0.00000
protocols.moves.TrialCounter: WeightedFragment trials=    399;  accepts= 0.0476;  energy_drop/trial=  -0.01318
protocols.hybridization.FoldTreeHybridize: Stage 4 loop iteration 3: small fragments smooth trials
protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 7218.91 7218.91
protocols.moves.TrialCounter:  ChunkTrialMover trials=      5;  accepts= 0.6000;  energy_drop/trial=  -0.15344
protocols.moves.TrialCounter: WeightedFragment trials=    395;  accepts= 0.0582;  energy_drop/trial=  -0.05075
core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 1
core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 22 to 1
protocols.hybridization.HybridizeProtocol: Realigning template domains to stage1 pose.
core.util.switchresiduetypeset: [ WARNING ] When switching to a centroid ResidueTypeSet:  Pose already contains centroid ResidueTypes.
protocols.hybridization.CartesianHybridize: RUNNING FOR 4 MACROCYCLES
protocols.hybridization.CartesianHybridize:  total_res=587   prot_res=587
protocols.hybridization.CartesianHybridize: CYCLE 1
protocols.hybridization.CartesianHybridize:   setting bonded weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded angle weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded length weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded torsion weight = 0
protocols.hybridization.CartesianHybridize:   setting cst    weight = 0.5
protocols.hybridization.CartesianHybridize:   setting vdw    weight = 0.1
core.energy_methods.CartesianBondedEnergy: Creating new peptide-bonded energy container (587)
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: CA,N,H to DB with theta0 = 2.07956 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: N,CA,C to DB with theta0 = 1.94081 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: N,CA,CB to DB with theta0 = 1.92861 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: N,CA,CEN to DB with theta0 = 1.9856 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: C,CA,CB to DB with theta0 = 1.92174 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: C,CA,CEN to DB with theta0 = 2.12444 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: CB,CA,CEN to DB with theta0 = 0.317107 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: CA,C,O to DB with theta0 = 2.10836 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: N,CA, to DB with d0 = 1.458 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: N,H, to DB with d0 = 1.01 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: CA,C, to DB with d0 = 1.52326 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: CA,CB, to DB with d0 = 1.52951 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: CA,CEN, to DB with d0 = 3.51447 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined length ORN: C,O, to DB with d0 = 1.23101 , Kd = 300
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: C,N,CA to DB with theta0 = 2.12407 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: CB,CA,C to DB with theta0 = 1.92174 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: CA,C,N to DB with theta0 = 2.02807 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: O,C,N to DB with theta0 = 2.14676 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: CA,N,C to DB with theta0 = 2.12407 , Ktheta = 80
core.energy_methods.CartesianBondedEnergy: Adding undefined angle ORN: H,N,C to DB with theta0 = 2.07956 , Ktheta = 80


AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

======================================================================================================================================

Crash.log:

[END_BACKTRACE]

[FILE]: SIGSEGV
[LINE]: 11
[START_MESSAGE]
Segmentation Fault

[END_MESSAGE]
[END_CRASH_REPORT]

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Thanks in advanced.

ac

 

 

Thu, 2022-07-28 02:09
adriancmf25

Hi ac,

 

I got the same crash. Were you able to fix this error later on?

 

Best,

jxw

Wed, 2023-10-11 10:04
jxw