Rosetta scripts crash in CM workflow

[Anonymous]

I’m trying to get started with comparative modeling for soluble proteins. I tried working through the demo/tutorial for membrane protein and adjusting for soluble, then also tried working with the RosettaCM workflow (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM). I’m having no trouble creating the input files, but seem to keep getting crashes at the step of calling rosetta_scripts.

I’m sure I am missing something, but am sort of stuck at the HybridizeMover step. Any thoughts would be great.

Thanks

 

Both rosetta_scripts.default.macosclangrelease and rosetta_scripts.macosclangrelease result in similar output in the crash log:

##############################################################################################################

#

# Rosetta crash log.

#

[START_CRASH_REPORT]

[ROSETTA_VERSION]: 2019.42+release.36665092fdf

[COMMIT_DATE]: 2019-10-21T22:51:57.839509

[APPLICATION]: /Users/burkheadjl/Desktop/Rosetta/main/source/bin/rosetta_scripts.macosclangrelease

[MODE]: Release

[EXTRAS]: default

[OS]: Apple Mac OS X

[COMPILER]: Clang version “10.0.0 (clang-1000.10.44.4)”

[STDLIB]: libc++ version 6000

[START_OPTIONS]

 -in:path:database=/Users/burkheadjl/Desktop/Rosetta/main/database/ -in:file:fasta=1cd1.fasta -parser:protocol=hybridize.xml -optimization:default_max_cycles=200 -relax:dualspace

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC

1   libutility.dylib                    0x000000010a591b68 utility::signal_handler(int) + 312

2   libsystem_platform.dylib            0x00007fff778dbf5a _sigtramp + 26

3   ???                                 0x3fee2a1e7d02fe9e 0x0 + 4606665779281329822

4   libcore.2.dylib                     0x0000000109781bfe core::conformation::carbohydrates::get_glycosidic_bond_residues(core::conformation::Conformation const&, unsigned long) + 574

5   libcore.2.dylib                     0x0000000109781e2c core::conformation::carbohydrates::get_reference_atoms_for_phi(core::conformation::Conformation const&, unsigned long) + 60

6   libcore.2.dylib                     0x0000000109783293 core::conformation::carbohydrates::get_reference_atoms(unsigned long, core::conformation::Conformation const&, unsigned long) + 99

7   libcore.2.dylib                     0x0000000109785ee9 core::conformation::carbohydrates::set_glycosidic_torsion(unsigned long, core::conformation::Conformation&, unsigned long, double) + 41

8   libprotocols.3.dylib                0x00000001059bc86e protocols::loops::set_extended_torsions_and_idealize_loops(core::pose::Pose&, protocols::loops::Loops) + 318

9   libprotocols.4.dylib                0x0000000104b580bd protocols::pose_creation::ExtendedPoseMover::apply(core::pose::Pose&) + 109

10  libprotocols_g.5.dylib              0x0000000103a16579 protocols::comparative_modeling::GenericJobInputter::pose_from_job(core::pose::Pose&, std::__1::shared_ptr<protocols::jd2::Job>) + 1257

11  libprotocols.1.dylib                0x0000000106818ce8 protocols::jd2::JobDistributor::run_one_job(std::__1::shared_ptr<protocols::moves::Mover>&, long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, unsigned long&, unsigned long&, bool) + 2072

12  libprotocols.1.dylib                0x0000000106817813 protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 195

13  libprotocols.1.dylib                0x00000001068121e6 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 70

14  rosetta_scripts.macosclangrelease   0x0000000100acb966 main + 1206

15  libdyld.dylib                       0x00007fff775cd015 start + 1

[END_BACKTRACE]

[FILE]: SIGSEGV

[LINE]: 11

[START_MESSAGE]

Segmentation Fault

[END_MESSAGE]

[END_CRASH_REPORT]

[Anonymous]

if you can, post the full xml  (preferebly in a code snippet or an attatchment will do) and your logs:

to get your logs run with your rosetta_scripts command and add “> out.log” (without the ” marks) and post the out.log file.

 

I’ve seen this exact error before I just forget what the problem was (usually a problem with your inputs in some fashion)

[Author]

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