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rosetta.script segmentation fault

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rosetta.script segmentation fault
#1

Dear all,

I am trying to perform a comparative homology modelling with the following command line

rosetta_scripts.linuxgccdebug @flags -database ~/rosetta_2013wk36_bundle/main/database/ -nstruct 10

the rosetta scripts is:

the error at the end of the output is:

core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (82)
rosetta_scripts.linuxgccdebug: src/utility/vectorL.hh:363: typename std::vector::reference utility::vectorL<, T, A>::operator[](typename utility::vectorL_IndexSelector<(L >= 0)>::index_type) [with int L = 1, T = utility::pointer::owning_ptr, A = std::allocator >]: Assertion `static_cast< size_type >( i - l_ ) < super::size()' failed.
Got some signal... It is:6
Process was aborted!

I can't understand why I get this error

thanks in advance for any help

felipet

Post Situation: 
Wed, 2013-10-02 10:41
felipet

felipet, can you post your script?

Wed, 2013-10-02 11:45
jadolfbr

I also tried the pdb and alignment of the CM threading example in the test folder and it works,

thanks

felipet

Fri, 2013-10-04 12:39
felipet

sorry,

the script is attached

and the flags I am using are:
# i/o
-in:file:fasta Inputs/t000_.fasta
-in:file:psipred_ss2 Inputs/t000_.psipred_ss2
-in:file:frag9 Inputs/aat000_09_05.200_v1_3
-in:file:frag3 Inputs/aat000_03_05.200_v1_3
-nstruct 10
-parser:protocol rosetta_cm.xml
-out:file:silent_struct_type binary

# relax options
-relax:minimize_bond_angles
-relax:minimize_bond_lengths
-relax:jump_move true
-default_max_cycles 200
-relax:min_type lbfgs_armijo_nonmonotone
-relax:jump_move true
-score:weights stage3_rlx.wts
-use_bicubic_interpolation
-hybridize:stage1_probability 1.0
-sog_upper_bound 15
#-mute all

# reduce memory footprint
-chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated
_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodin
ated N_acetylated C_methylamidated MethylatedProteinCterm

Wed, 2013-10-02 12:08
felipet

Filipet, are you a developer?
I've never used homology modelling in Rosetta; however the issue you are seeing looks to be coming from the CartesianMinimizer. Are you using 3.5/weekly or the developers trunk?

If you remove these options, your bug should go away.
-relax:minimize_bond_angles
-relax:minimize_bond_lengths

Frank Dimaio may be be able to help, as he wrote most of the Cartesian code.
http://pages.cs.wisc.edu/~dimaio/

Mon, 2013-10-14 08:31
jadolfbr