rosetta_cm segfault

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    • #3808
      Anonymous

        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]

         

         

         

         

      • #15968
        Anonymous

          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>

           

           

        • #15969
          Anonymous

            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.

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