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rosetta_cm segfault

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rosetta_cm segfault
#1

I set up a homology model with the setup_RosettaCM.py
It creates a set of threaded models, an xml file with commands, and a flags command that points to the input file and the xml. When I run the rosetta_scripts command with this flags and xml, I get a segmentation fault. I find the error messages difficult to understand. 

Here is the command, screen output, flags, xml, and CRASH.log

 /workgroups/bio/apps/rosetta/3.12/main/source/bin//rosetta_scripts.default.linuxgccrelease @flags -database /workgroups/bio/apps/rosetta/3.12/main/database -nstruct 20

 

$  /workgroups/bio/apps/rosetta/3.12/main/source/bin//rosetta_scripts.default.linuxgccrelease @flags -database /workgroups/bio/apps/rosetta/3.12/main/database -nstruct 20
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.source.release-247 r247 2020.08+release.cb1caba cb1cabafd7463ab703f6abf5efa33d2707b85924 https://www.rosettacommons.org 2020-02-22T18:49:33.865989
core.init: command: /workgroups/bio/apps/rosetta/3.12/main/source/bin//rosetta_scripts.default.linuxgccrelease @flags -database /workgroups/bio/apps/rosetta/3.12/main/database -nstruct 20
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-124808577 seed_offset=0 real_seed=-124808577
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-124808577 RG_type=mt19937
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set.  Created 62 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.04 seconds.


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

Segmentation fault
 

$cat flags

# i/o
-in:file:fasta ANME2_HR1.fasta
-nstruct 20
-parser:protocol rosetta_cm.xml

# relax options
-relax:dualspace
-relax:jump_move true
-default_max_cycles 200
-hybridize:stage1_probability 1.0


##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-22T18:49:33.865989
[APPLICATION]: /workgroups/bio/apps/rosetta/3.12/main/source/bin//rosetta_scripts.default.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "8.2.0"
[STDLIB]: libstdc++ version 20180726
[START_OPTIONS]
 -in:path:database=/workgroups/bio/apps/rosetta/3.12/main/database/ -in:file:fasta=ANME2_HR1.fasta -out:nstruct=20 -parser:protocol=rosetta_cm.xml -
optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:dualspace -relax:jump_move

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libutility.so(utility::save_crash_report(char
 const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x23) [0x7f9e3aa642b3]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libutility.so(utility::signal_handler(int)+0x
d4) [0x7f9e3aa643c4]
/lib64/libc.so.6(+0x36340) [0x7f9e389bc340]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libcore.2.so(core::conformation::carbohydrate
s::find_seqpos_of_saccharides_parent_residue(core::conformation::Residue const&)+0x36) [0x7f9e3c2a1146]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libcore.2.so(core::conformation::carbohydrate
s::get_glycosidic_bond_residues(core::conformation::Conformation const&, unsigned long)+0x508) [0x7f9e3c2a5a48]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libcore.2.so(core::conformation::carbohydrate
s::get_reference_atoms_for_phi(core::conformation::Conformation const&, unsigned long)+0x47) [0x7f9e3c2a5d57]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libcore.2.so(core::conformation::carbohydrate
s::get_reference_atoms(unsigned long, core::conformation::Conformation const&, unsigned long)+0x248) [0x7f9e3c2aa978]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libcore.2.so(core::conformation::carbohydrate
s::set_glycosidic_torsion(unsigned long, core::conformation::Conformation&, unsigned long, double)+0x24) [0x7f9e3c2ac374]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libcore.3.so(core::pose::Pose::set_phi(unsign
ed long, double)+0x288) [0x7f9e3d139408]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libprotocols.3.so(protocols::loops::set_exten
ded_torsions_and_idealize_loops(core::pose::Pose&, protocols::loops::Loops)+0xce) [0x7f9e4230960e]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libprotocols.4.so(protocols::pose_creation::E
xtendedPoseMover::apply(core::pose::Pose&)+0x6b) [0x7f9e43d6b8db]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libprotocols_g.5.so(protocols::comparative_mo
deling::GenericJobInputter::pose_from_job(core::pose::Pose&, std::shared_ptr<protocols::jd2::Job>)+0xd6a) [0x7f9e46188cfa]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libprotocols.1.so(protocols::jd2::JobDistribu
tor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0x1d8c) [0x7f9e40b952fc]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libprotocols.1.so(protocols::jd2::JobDistribu
tor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x14e) [0x7f9e40b95e6e]
/weka/workgroups/bio/apps/rosetta/3.12/main/source/build/src/release/linux/3.10/64/x86/gcc/8.2/default/libprotocols.1.so(protocols::jd2::FileSystemJ
obDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x47) [0x7f9e40b7e707]
/workgroups/bio/apps/rosetta/3.12/main/source/bin//rosetta_scripts.default.linuxgccrelease() [0x402383]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f9e389a8495]
/workgroups/bio/apps/rosetta/3.12/main/source/bin//rosetta_scripts.default.linuxgccrelease() [0x4025fe]

[END_BACKTRACE]

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

[END_MESSAGE]
[END_CRASH_REPORT]
 

 

 

 

Post Situation: 
Fri, 2021-07-09 13:35
browns02

here is the xml

<ROSETTASCRIPTS>
    <TASKOPERATIONS>
    </TASKOPERATIONS>
    <SCOREFXNS>
        <ScoreFunction name="stage1" weights="score3" symmetric="0">
            <Reweight scoretype="atom_pair_constraint" weight="0.1"/>
        </ScoreFunction>
        <ScoreFunction name="stage2" weights="score4_smooth_cart" symmetric="0">
            <Reweight scoretype="atom_pair_constraint" weight="0.1"/>
        </ScoreFunction>
        <ScoreFunction name="fullatom" weights="beta_cart" symmetric="0">
            <Reweight scoretype="atom_pair_constraint" weight="0.1"/>
        </ScoreFunction>
    </SCOREFXNS>
    <FILTERS>
    </FILTERS>
    <MOVERS>
        <Hybridize name="hybridize" stage1_scorefxn="stage1" stage2_scorefxn="stage2" fa_scorefxn="fullatom" batch="1" stage1_increase_cycles="1.0" stage2_increase_cycles="1.0">
            <Template pdb="/weka/workgroups/bio/Rosetta/MCR/rosetta_cm/1E6Y__thread.pdb" cst_file="AUTO" weight="1.0" />
            <Template pdb="/weka/workgroups/bio/Rosetta/MCR/rosetta_cm/7NKG__thread.pdb" cst_file="AUTO" weight="1.0" />
            <Template pdb="/weka/workgroups/bio/Rosetta/MCR/rosetta_cm/1E6V__thread.pdb" cst_file="AUTO" weight="1.0" />
        </Hybridize>
    </MOVERS>
    <APPLY_TO_POSE>
    </APPLY_TO_POSE>
    <PROTOCOLS>
        <Add mover="hybridize"/>
    </PROTOCOLS>
</ROSETTASCRIPTS>
 

 

Fri, 2021-07-09 13:37
browns02

Passing on a comment from a RosettaCM expert: "this is almost certainly windows newlines in the fasta".

I recommend using something like the `dos2unix` utility that comes with most Linux OSs to normalize the file, and see if that helps.

Fri, 2021-07-09 15:05
rmoretti