core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/bin/minirosetta.linuxgccrelease @/home/lanselibai/Cheng/Rosetta_run/20150210_minirosetta/input/comparative_model_4KMT_to_C226S.options -database /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/database core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1221661885 seed_offset=0 real_seed=-1221661885 core.init.random: RandomGenerator:init: Normal mode, seed=-1221661885 RG_type=mt19937 protocols.loops.loops_main: Frag libraries debug /home/lanselibai/Cheng/Rosetta_run/20150210_minirosetta/input/aaC226S_09_05.200_v1_3 9 core.io.fragments: reading fragments from file: /home/lanselibai/Cheng/Rosetta_run/20150210_minirosetta/input/aaC226S_09_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file /home/lanselibai/Cheng/Rosetta_run/20150210_minirosetta/input/aaC226S_09_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug /home/lanselibai/Cheng/Rosetta_run/20150210_minirosetta/input/aaC226S_03_05.200_v1_3 3 core.io.fragments: reading fragments from file: /home/lanselibai/Cheng/Rosetta_run/20150210_minirosetta/input/aaC226S_03_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file /home/lanselibai/Cheng/Rosetta_run/20150210_minirosetta/input/aaC226S_03_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug none 1 protocols.loops.loops_main: Set up 1-mer library from 3-mer library protocols.loops.loops_main: Fragment libraries: 1 264000 protocols.loops.loops_main: Fragment libraries: 3 88000 protocols.loops.loops_main: Fragment libraries: 9 86800 core.chemical.ResidueProperties: Rosetta does not recognize the variant: UPPER_TERMINUS; has it been added to variant_types.list? core.chemical.ResidueProperties: Rosetta does not recognize the variant: UPPERTERM_TRUNC; has it been added to variant_types.list? core.chemical.ResidueProperties: Rosetta does not recognize the variant: UPPER_TERMINUS; has it been added to variant_types.list? core.chemical.ResidueProperties: Rosetta does not recognize the variant: UPPERTERM_TRUNC; has it been added to variant_types.list? core.chemical.ResidueProperties: Rosetta does not recognize the variant: UPPER_TERMINUS; has it been added to variant_types.list? core.chemical.ResidueProperties: Rosetta does not recognize the variant: UPPERTERM_TRUNC; has it been added to variant_types.list? ERROR: Rosetta does not recognize the variant: UPPER_TERMINUS; has it been added to variant_types.list? ERROR:: Exit from: src/core/chemical/ResidueProperties.cc line: 145 /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libutility.so(print_backtrace()+0x26) [0x7f4aba5186e6] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0xd4) [0x7f4aba518444] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libcore.2.so(core::chemical::ResidueProperties::set_variant_type(std::string const&, bool)+0x15f) [0x7f4ab6a5ee0f] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libcore.2.so(core::chemical::Patch::apply(core::chemical::ResidueType const&) const+0x382) [0x7f4ab6a21462] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libcore.2.so(core::chemical::ResidueTypeSet::apply_patches(utility::vector1 > const&)+0x3c2) [0x7f4ab6ab2d82] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libcore.2.so(core::chemical::ResidueTypeSet::init(std::vector > const&, std::vector > const&)+0x13f3) [0x7f4ab6ab6db3] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libcore.2.so(core::chemical::ChemicalManager::create_residue_type_set(std::string const&) const+0x3f1) [0x7f4ab69ef8f1] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libcore.2.so(boost::detail::function::function_obj_invoker0, boost::_mfi::cmf1, core::chemical::ChemicalManager, std::string const&>, boost::_bi::list2, boost::reference_wrapper > >, boost::shared_ptr >::invoke(boost::detail::function::function_buffer&)+0x27) [0x7f4ab69f3457] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libcore.2.so(core::chemical::ChemicalManager::residue_type_set(std::string)+0x24b) [0x7f4ab69eef7b] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::poseOPs_from_pdbs(utility::vector1 > const&, core::import_pose::ImportPoseOptions const&, bool)+0xe8) [0x7f4ab90a6fc8] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::poseOPs_from_pdbs(utility::vector1 > const&, bool)+0x33) [0x7f4ab90a76b3] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libprotocols_g.4.so(protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter()+0x358) [0x7f4abd68c298] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libprotocols_g.4.so(protocols::comparative_modeling::ThreadingJobInputterCreator::create_JobInputter() const+0x1e) [0x7f4abd68d35e] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobInputterFactory::get_JobInputter_from_string(std::string const&)+0x43) [0x7f4abb251203] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobInputterFactory::get_new_JobInputter()+0x4a2) [0x7f4abb251842] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributorFactory::create_job_inputter()+0x21) [0x7f4abb250691] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::init_jd()+0x19d) [0x7f4abb24f58d] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::JobDistributor()+0xe0) [0x7f4abb24fc00] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::FileSystemJobDistributor()+0x14) [0x7f4abb22f184] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributorFactory::create_job_distributor()+0x1b3) [0x7f4abb250ab3] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::get_instance()+0x128) [0x7f4abb24ebb8] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.13/64/x86/gcc/4.8/default/libprotocols_g.4.so(protocols::comparative_modeling::cm_main()+0x103) [0x7f4abd649b33] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/bin/minirosetta.linuxgccrelease() [0x403a56] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f4ab99f7ec5] /home/lanselibai/Cheng/rosetta_src_2015.05.57576_bundle/main/source/bin/minirosetta.linuxgccrelease() [0x40403d]