Conda version '22.9.0' loaded
Not necessary to setup conda init now
/usr/share/lmod/lmod/init/bash: line 70: activate: No such file or directory
core.init: Rosetta version: rosetta.binary.linux.release-171 r171 2018.09+release.333d996 333d99699777cd6a50d1c1736bacd689f8f1d1df https://www.rosettacommons.org 2018-02-27T09:57:00.705373
core.init: command: rifgen @rifgen.flags
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1753438411 seed_offset=0 real_seed=-1753438411
core.init.random: RandomGenerator:init: Normal mode, seed=-1753438411 RG_type=mt19937
core.init: Resolved executable path: /research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/rifdock/vendor/rifdock/build/apps/rosetta/rifgen
core.init: Looking for database based on location of executable: /research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/rifdock/vendor/rifdock/build/apps/rosetta/../database/
Rifdock thinks there are 16 threads.
rif_type: RotScore64
does not exist, attempting to create:
    rifgen_4S0U

=================================================== preparing target ===================================================


ERROR: ResidueType::add_ring: Requested atoms don't exist in this ResidueType!
ERROR:: Exit from: /research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/src/core/chemical/ResidueType.cc line: 1744
BACKTRACE:
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x2cd) [0x2aaabbd649cd]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::ResidueType::add_ring(unsigned long, utility::vector1<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)+0x83f) [0x2aaaabe943ff]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::read_topology_file(std::istream&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::weak_ptr<core::chemical::AtomTypeSet const>, std::weak_ptr<core::chemical::ElementSet const>, std::weak_ptr<core::chemical::MMAtomTypeSet const>, std::weak_ptr<core::chemical::orbitals::OrbitalTypeSet const>)+0x2efc) [0x2aaaabf4a5dc]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::read_topology_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::weak_ptr<core::chemical::AtomTypeSet const>, std::weak_ptr<core::chemical::ElementSet const>, std::weak_ptr<core::chemical::MMAtomTypeSet const>, std::weak_ptr<core::chemical::orbitals::OrbitalTypeSet const>)+0x29f) [0x2aaaabf4e22f]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::GlobalResidueTypeSet::init_restypes_from_database()+0x8e3) [0x2aaaabdd5d23]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::GlobalResidueTypeSet::GlobalResidueTypeSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x1a1) [0x2aaaabde2841]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::ChemicalManager::create_residue_type_set(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const+0x207) [0x2aaaabdbc887]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.2.so(boost::detail::function::function_obj_invoker0<boost::_bi::bind_t<std::shared_ptr<core::chemical::GlobalResidueTypeSet>, boost::_mfi::cmf1<std::shared_ptr<core::chemical::GlobalResidueTypeSet>, core::chemical::ChemicalManager, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>, boost::_bi::list2<boost::_bi::value<core::chemical::ChemicalManager*>, boost::reference_wrapper<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const> > >, std::shared_ptr<core::chemical::GlobalResidueTypeSet> >::invoke(boost::detail::function::function_buffer&)+0x2a) [0x2aaaabdc38ca]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::ChemicalManager::residue_type_set(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x2b2) [0x2aaaabdc0c42]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::ChemicalManager::residue_type_set(core::chemical::TypeSetMode)+0x29) [0x2aaaabdc1449]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.2.so(core::conformation::Conformation::residue_type_set_for_conf(core::chemical::TypeSetMode) const+0xba) [0x2aaaabccf2ea]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.3.so(core::pose::Pose::residue_type_set_for_pose(core::chemical::TypeSetMode) const+0xd) [0x2aaaacdd45fd]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x7d) [0x2aaaafc3343d]
/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/cmake/build_cxx11_omp/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, core::import_pose::FileType)+0x3a) [0x2aaaafc3350a]
rifgen(main+0x707) [0x4332b7]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2aaabd706555]
rifgen() [0x4399ce]
terminate called after throwing an instance of 'utility::UtilityExitException'
  what():  

File: /research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/rosetta/vendor/2018.09.60072/main/source/src/core/chemical/ResidueType.cc:1744
[ ERROR ] UtilityExitException
ERROR: ResidueType::add_ring: Requested atoms don't exist in this ResidueType!


/lsf_jobspool/1689870724.197049883.shell: line 14: 34167 Aborted                 (core dumped) rifgen @rifgen.flags

------------------------------------------------------------
Sender: LSF System <lsfadmin@noderome267>
Subject: Job 197049883: <rifgen> in cluster <hpcf_research_cluster> Exited

Job <rifgen> was submitted from host <splprhpc07> by user <wabualaadmin> in cluster <hpcf_research_cluster> at Thu Jul 20 11:32:04 2023
Job was executed on host(s) <16*noderome267>, in queue <standard>, as user <wabualaadmin> in cluster <hpcf_research_cluster> at Thu Jul 20 11:32:10 2023
</home/wabualaadmin> was used as the home directory.
</home/wabualaadmin/rifdock_mat> was used as the working directory.
Started at Thu Jul 20 11:32:10 2023
Terminated at Thu Jul 20 11:32:50 2023
Results reported at Thu Jul 20 11:32:50 2023

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
#!/bin/bash

#BSUB -J rifgen
#BSUB -P rifgentest
#BSUB -q standard
#BSUB -n 16
#BSUB -R "rusage[mem=4096]"
#BSUB -o rifgen5.log

export WORKDIR=$PWD

module load rifdock

rifgen @rifgen.flags

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

Exited with exit code 134.

Resource usage summary:

    CPU time :                                   3.69 sec.
    Max Memory :                                 26 MB
    Average Memory :                             17.80 MB
    Total Requested Memory :                     65536.00 MB
    Delta Memory :                               65510.00 MB
    Max Swap :                                   -
    Max Processes :                              5
    Max Threads :                                6
    Run time :                                   39 sec.
    Turnaround time :                            46 sec.

The output (if any) is above this job summary.