############################################################################################################## # # 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]: 2020-02-21T14:46:08.581859 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)" [STDLIB]: libstdc++ version 20150623 [START_OPTIONS] -in:path:database=/path/to/Rosetta/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC [0x3a91d6f] [0x5fe5ef3] [0x608c3d6] [0x59d8b0a] [0x59e421a] [0x59cdf94] [0x59cea27] [0x59cc1f8] [0x45ed5f4] [0x265c340] [0x1d973fd] [0x393cab1] [0x393ebc1] [0x39d8148] [0x411fcb] [0x65816d4] [0x630dfd] [END_BACKTRACE] [FILE]: src/core/chemical/GlobalResidueTypeSet.cc [LINE]: 148 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: Unable to open file: /path/to/Rosetta/main/database/chemical/residue_type_sets/centroid/residue_types.txt [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2020-02-21T14:46:08.581859 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)" [STDLIB]: libstdc++ version 20150623 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC [0x6089b2c] [0x6589d50] [0x586b91e] [0x586d000] [0x586d0c8] [0x586f2d9] [0x586f841] [0x461cd38] [0x321eb1e] [0x265c35c] [0x1d973fd] [0x393cab1] [0x393ebc1] [0x39d8148] [0x411fcb] [0x65816d4] [0x630dfd] [END_BACKTRACE] [FILE]: SIGSEGV [LINE]: 11 [START_MESSAGE] Segmentation Fault [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2020-02-21T14:46:08.581859 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)" [STDLIB]: libstdc++ version 20150623 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC [0x6089b2c] [0x6589d50] [0x586b91e] [0x586d000] [0x586d0c8] [0x586f2d9] [0x586f841] [0x461cd38] [0x321eb1e] [0x265c35c] [0x1d973fd] [0x393cab1] [0x393ebc1] [0x39d8148] [0x411fcb] [0x65816d4] [0x630dfd] [END_BACKTRACE] [FILE]: SIGSEGV [LINE]: 11 [START_MESSAGE] Segmentation Fault [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2020-02-21T14:46:08.581859 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string, std::allocator > const&, int)+0x38) [0x7f724b3d45c8] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::signal_handler(int)+0xe8) [0x7f724b3d4708] /lib/x86_64-linux-gnu/libc.so.6(+0x430c0) [0x7f724ae630c0] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.2.so(core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(core::conformation::Residue const&)+0x4a) [0x7f7242d725aa] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.2.so(core::conformation::carbohydrates::get_glycosidic_bond_residues(core::conformation::Conformation const&, unsigned long)+0x518) [0x7f7242d77d88] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.2.so(core::conformation::carbohydrates::get_reference_atoms_for_phi(core::conformation::Conformation const&, unsigned long)+0x5e) [0x7f7242d7808e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.2.so(core::conformation::carbohydrates::get_reference_atoms(unsigned long, core::conformation::Conformation const&, unsigned long)+0x4bb) [0x7f7242d7d29b] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.2.so(core::conformation::carbohydrates::set_glycosidic_torsion(unsigned long, core::conformation::Conformation&, unsigned long, double)+0x38) [0x7f7242d7e118] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::pose::Pose::set_phi(unsigned long, double)+0x2c0) [0x7f7243b1e010] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols.3.so(protocols::loops::set_extended_torsions_and_idealize_loops(core::pose::Pose&, protocols::loops::Loops)+0xda) [0x7f724783551a] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols.4.so(protocols::pose_creation::ExtendedPoseMover::apply(core::pose::Pose&)+0x82) [0x7f72492b01c2] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols_g.5.so(protocols::comparative_modeling::GenericJobInputter::pose_from_job(core::pose::Pose&, std::shared_ptr)+0x936) [0x7f724975dca6] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr&, long, std::__cxx11::basic_string, std::allocator >&, std::__cxx11::basic_string, std::allocator >&, unsigned long&, unsigned long&, bool)+0x1d4d) [0x7f724c19463d] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x23d) [0x7f724c19641d] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x57) [0x7f724c17d677] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease(+0x284a) [0x7f724d52684a] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f724ae440b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease(+0x2b4e) [0x7f724d526b4e] [END_BACKTRACE] [FILE]: SIGSEGV [LINE]: 11 [START_MESSAGE] Segmentation Fault [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2020-02-21T14:46:08.581859 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string, std::allocator > const&, int)+0x38) [0x7f132d6c45c8] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::signal_handler(int)+0xe8) [0x7f132d6c4708] /lib/x86_64-linux-gnu/libc.so.6(+0x430c0) [0x7f132d1530c0] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.2.so(core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(core::conformation::Residue const&)+0x4a) [0x7f13250625aa] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.2.so(core::conformation::carbohydrates::get_glycosidic_bond_residues(core::conformation::Conformation const&, unsigned long)+0x518) [0x7f1325067d88] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.2.so(core::conformation::carbohydrates::get_reference_atoms_for_phi(core::conformation::Conformation const&, unsigned long)+0x5e) [0x7f132506808e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.2.so(core::conformation::carbohydrates::get_reference_atoms(unsigned long, core::conformation::Conformation const&, unsigned long)+0x4bb) [0x7f132506d29b] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.2.so(core::conformation::carbohydrates::set_glycosidic_torsion(unsigned long, core::conformation::Conformation&, unsigned long, double)+0x38) [0x7f132506e118] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::pose::Pose::set_phi(unsigned long, double)+0x2c0) [0x7f1325e0e010] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols.3.so(protocols::loops::set_extended_torsions_and_idealize_loops(core::pose::Pose&, protocols::loops::Loops)+0xda) [0x7f1329b2551a] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols.4.so(protocols::pose_creation::ExtendedPoseMover::apply(core::pose::Pose&)+0x82) [0x7f132b5a01c2] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols_g.5.so(protocols::comparative_modeling::GenericJobInputter::pose_from_job(core::pose::Pose&, std::shared_ptr)+0x936) [0x7f132ba4dca6] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr&, long, std::__cxx11::basic_string, std::allocator >&, std::__cxx11::basic_string, std::allocator >&, unsigned long&, unsigned long&, bool)+0x1d4d) [0x7f132e48463d] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x23d) [0x7f132e48641d] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x57) [0x7f132e46d677] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.linuxgccrelease(+0x284a) [0x7f132f81784a] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f132d1340b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.linuxgccrelease(+0x2b4e) [0x7f132f817b4e] [END_BACKTRACE] [FILE]: SIGSEGV [LINE]: 11 [START_MESSAGE] Segmentation Fault [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2021.07+release.c48be26 [COMMIT_DATE]: 2021-02-22T05:58:26.229012 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug [MODE]: Debug [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f1503c58b59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xb2) [0x7f1503cb7e4e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::file_contents(std::__cxx11::basic_string, std::allocator > const&)+0xf1) [0x7f1503c9eeb6] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libbasic.so(basic::citation_manager::CitationManager::load_rosetta_citations_from_database()+0x9f) [0x7f150486a705] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libbasic.so(basic::citation_manager::CitationManager::CitationManager()+0x45) [0x7f1504869cb7] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(utility::SingletonBase::get_instance()+0x42) [0x7f1508fcf78b] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1186a) [0x7f1508fcd86a] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f1502a740b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1166e) [0x7f1508fcd66e] [END_BACKTRACE] [FILE]: src/utility/string_util.cc [LINE]: 550 [START_MESSAGE] Could not open file /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations.txt [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2021.07+release.c48be26 [COMMIT_DATE]: 2021-02-22T05:58:26.229012 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug [MODE]: Debug [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f769ded8b59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xb2) [0x7f769df37e4e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::file_contents(std::__cxx11::basic_string, std::allocator > const&)+0xf1) [0x7f769df1eeb6] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libbasic.so(basic::citation_manager::CitationManager::load_rosetta_citations_from_database()+0x9f) [0x7f769eaea705] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libbasic.so(basic::citation_manager::CitationManager::CitationManager()+0x45) [0x7f769eae9cb7] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(utility::SingletonBase::get_instance()+0x42) [0x7f76a325478b] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1186a) [0x7f76a325286a] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f769ccf40b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1166e) [0x7f76a325266e] [END_BACKTRACE] [FILE]: src/utility/string_util.cc [LINE]: 550 [START_MESSAGE] Could not open file /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations.txt [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2021.07+release.c48be26 [COMMIT_DATE]: 2021-02-22T05:58:26.229012 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug [MODE]: Debug [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7fdf6be98b59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xb2) [0x7fdf6bef7e4e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::file_contents(std::__cxx11::basic_string, std::allocator > const&)+0xf1) [0x7fdf6bedeeb6] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libbasic.so(basic::citation_manager::CitationManager::load_rosetta_citations_from_database()+0x9f) [0x7fdf6caaa705] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libbasic.so(basic::citation_manager::CitationManager::CitationManager()+0x45) [0x7fdf6caa9cb7] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(utility::SingletonBase::get_instance()+0x42) [0x7fdf7121478b] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1186a) [0x7fdf7121286a] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7fdf6acb40b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1166e) [0x7fdf7121266e] [END_BACKTRACE] [FILE]: src/utility/string_util.cc [LINE]: 550 [START_MESSAGE] Could not open file /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations.txt [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2021.07+release.c48be26 [COMMIT_DATE]: 2021-02-22T05:58:26.229012 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug [MODE]: Debug [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f41cdd08b59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xb2) [0x7f41cdd67e4e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::file_contents(std::__cxx11::basic_string, std::allocator > const&)+0xf1) [0x7f41cdd4eeb6] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libbasic.so(basic::citation_manager::CitationManager::load_rosetta_citations_from_database()+0x9f) [0x7f41ce915705] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libbasic.so(basic::citation_manager::CitationManager::CitationManager()+0x45) [0x7f41ce914cb7] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(utility::SingletonBase::get_instance()+0x42) [0x7f41d307878b] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1186a) [0x7f41d307686a] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f41ccb240b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1166e) [0x7f41d307666e] [END_BACKTRACE] [FILE]: src/utility/string_util.cc [LINE]: 550 [START_MESSAGE] Could not open file /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations.txt [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2021.07+release.c48be26 [COMMIT_DATE]: 2021-02-22T05:58:26.229012 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug [MODE]: Debug [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f8a00a08b59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xb2) [0x7f8a00a67e4e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::RosettaScriptsParser::validate_input_script_against_xsd(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator > const&) const+0x632) [0x7f8a035897d2] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::RosettaScriptsParser::finish_creating_tag(std::__cxx11::basic_string, std::allocator > const&, utility::vector1, std::allocator >, std::allocator, std::allocator > > > const&, std::__cxx11::basic_string, std::allocator > const&) const+0x144) [0x7f8a0357ebf8] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::RosettaScriptsParser::create_tag_from_xml(std::__cxx11::basic_string, std::allocator > const&, utility::vector1, std::allocator >, std::allocator, std::allocator > > > const&)+0x14f) [0x7f8a0357e7bd] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::RosettaScriptsParser::create_tag_from_xml(std::__cxx11::basic_string, std::allocator > const&, utility::options::OptionCollection const&)+0xea) [0x7f8a0357f0a0] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(std::shared_ptr&, bool, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, bool)+0x123) [0x7f8a035808fd] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr&, long, std::__cxx11::basic_string, std::allocator >&, std::__cxx11::basic_string, std::allocator >&, unsigned long&, unsigned long&, bool)+0xf35) [0x7f8a0303cd59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0xf6) [0x7f8a0303b07e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x59) [0x7f8a0302cbdd] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x11af4) [0x7f8a05d7caf4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f89ff8240b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1166e) [0x7f8a05d7c66e] [END_BACKTRACE] [FILE]: src/protocols/rosetta_scripts/RosettaScriptsParser.cc [LINE]: 1205 [START_MESSAGE] Input rosetta scripts XML file "rosetta_cm.xml" failed to validate against the rosetta scripts schema. Use the option -parser::output_schema to output the schema to a file to see all valid options. Your XML has failed validation. The error message below will tell you where in your XML file the error occurred. Here's how to fix it: 1) If the validation fails on something obvious, like an illegal attribute due to a spelling error (perhaps you used scorefnction instead of scorefunction), then you need to fix your XML file. 2) If you haven't run the XML rewriter script and this might be pre-2017 Rosetta XML, run the rewriter script (tools/xsd_xrw/rewrite_rosetta_script.py) on your input XML first. The attribute values not being in quotes (scorefunction=talaris2014 instead of scorefunction="talaris2014") is a good indicator that this is your problem. 3) If you are a developer and neither 1 nor 2 worked - email the developer's mailing list or try Slack. 4) If you are an academic or commercial user - try the Rosetta Forums https://www.rosettacommons.org/forum Error messages were: Error: AttValue: " or ' expected 1: 2: 3: 4: 5: 6: 7: 8: 9: 10: Error: attributes construct error 1: 2: 3: 4: 5: 6: 7: 8: 9: 10: Error: Couldn't find end of Start Tag stage1 line 5 1: 2: 3: 4: 5: 6: 7: 8: 9: 10: Error: AttValue: " or ' expected 1: 2: 3: 4: 5: 6: 7: 8: 9: 10: 11: Error: attributes construct error 1: 2: 3: 4: 5: 6: 7: 8: 9: 10: 11: Error: Couldn't find end of Start Tag Reweight line 6 1: 2: 3: 4: 5: 6: 7: 8: 9: 10: 11: Error: Opening and ending tag mismatch: SCOREFXNS line 4 and stage1 2: 3: 4: 5: 6: 7: 8: 9: 10: 11: 12: Error: AttValue: " or ' expected 3: 4: 5: 6: 7: 8: 9: 10: 11: 12: 13: Error: attributes construct error 3: 4: 5: 6: 7: 8: 9: 10: 11: 12: 13: Error: Couldn't find end of Start Tag stage2 line 8 3: 4: 5: 6: 7: 8: 9: 10: 11: 12: 13: Error: AttValue: " or ' expected 4: 5: 6: 7: 8: 9: 10: 11: 12: 13: 14: Error: attributes construct error 4: 5: 6: 7: 8: 9: 10: 11: 12: 13: 14: Error: Couldn't find end of Start Tag Reweight line 9 4: 5: 6: 7: 8: 9: 10: 11: 12: 13: 14: Error: Opening and ending tag mismatch: dock_design line 1 and stage2 5: 6: 7: 8: 9: 10: 11: 12: 13: 14: 15: Error: Extra content at the end of the document 6: 7: 8: 9: 10: 11: 12: 13: 14: 15: 16: ------------------------------------------------------------ Warning messages were: ------------------------------------------------------------ [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2021.07+release.c48be26 [COMMIT_DATE]: 2021-02-22T05:58:26.229012 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug [MODE]: Debug [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm_new.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7fe691dc8b59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xb2) [0x7fe691e27e4e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x76) [0x7fe691dcdf06] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x55) [0x7fe691dcd696] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunction::_add_weights_from_stream(std::istream&, bool, std::__cxx11::basic_string, std::allocator > const&)+0x1bf5) [0x7fe67d591ca3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunction::_add_weights_from_file(std::__cxx11::basic_string, std::allocator > const&, bool)+0xb2) [0x7fe67d590036] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunction::add_weights_from_file(std::__cxx11::basic_string, std::allocator > const&)+0x76) [0x7fe67d58fefa] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunction::initialize_from_file(std::__cxx11::basic_string, std::allocator > const&)+0x33) [0x7fe67d58f785] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunctionFactory::load_weights_file(std::__cxx11::basic_string, std::allocator >, std::shared_ptr)+0x32) [0x7fe67d5f74c6] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunctionFactory::create_score_function(utility::options::OptionCollection const&, std::__cxx11::basic_string, std::allocator > const&, utility::vector1, std::allocator >, std::allocator, std::allocator > > > const&)+0x3d6) [0x7fe67d5f5c9a] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::get_score_function(utility::options::OptionCollection const&, bool)+0x547) [0x7fe67d5f7b59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::RosettaScriptsParser::initialize_data_map(basic::datacache::DataMap&, utility::options::OptionCollection const&)+0xd6) [0x7fe69493a1e4] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(std::shared_ptr, utility::options::OptionCollection const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::shared_ptr, std::shared_ptr)+0x8e) [0x7fe69493badc] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(std::shared_ptr&, bool, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, bool)+0x197) [0x7fe69493b971] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr&, long, std::__cxx11::basic_string, std::allocator >&, std::__cxx11::basic_string, std::allocator >&, unsigned long&, unsigned long&, bool)+0xf35) [0x7fe6943f7d59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0xf6) [0x7fe6943f607e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x59) [0x7fe6943e7bdd] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x11af4) [0x7fe697134af4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7fe690be40b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1166e) [0x7fe69713466e] [END_BACKTRACE] [FILE]: src/core/scoring/ScoreFunction.cc [LINE]: 468 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: bad line in file stage3.wts:fa_plane 0 [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2021.07+release.c48be26 [COMMIT_DATE]: 2021-02-22T05:58:26.229012 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosettaDNA.default.linuxgccdebug [MODE]: Debug [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm_new.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f2eb97e8b59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xb2) [0x7f2eb9847e4e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x76) [0x7f2eb97edf06] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x55) [0x7f2eb97ed696] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunction::_add_weights_from_stream(std::istream&, bool, std::__cxx11::basic_string, std::allocator > const&)+0x1bf5) [0x7f2ea8e36ca3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunction::_add_weights_from_file(std::__cxx11::basic_string, std::allocator > const&, bool)+0xb2) [0x7f2ea8e35036] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunction::add_weights_from_file(std::__cxx11::basic_string, std::allocator > const&)+0x76) [0x7f2ea8e34efa] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunction::initialize_from_file(std::__cxx11::basic_string, std::allocator > const&)+0x33) [0x7f2ea8e34785] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunctionFactory::load_weights_file(std::__cxx11::basic_string, std::allocator >, std::shared_ptr)+0x32) [0x7f2ea8e9c4c6] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::ScoreFunctionFactory::create_score_function(utility::options::OptionCollection const&, std::__cxx11::basic_string, std::allocator > const&, utility::vector1, std::allocator >, std::allocator, std::allocator > > > const&)+0x3d6) [0x7f2ea8e9ac9a] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::get_score_function(utility::options::OptionCollection const&, bool)+0x547) [0x7f2ea8e9cb59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::RosettaScriptsParser::initialize_data_map(basic::datacache::DataMap&, utility::options::OptionCollection const&)+0xd6) [0x7f2ebc35f1e4] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(std::shared_ptr, utility::options::OptionCollection const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::shared_ptr, std::shared_ptr)+0x8e) [0x7f2ebc360adc] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(std::shared_ptr&, bool, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, bool)+0x197) [0x7f2ebc360971] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr&, long, std::__cxx11::basic_string, std::allocator >&, std::__cxx11::basic_string, std::allocator >&, unsigned long&, unsigned long&, bool)+0xf35) [0x7f2ebbe1cd59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0xf6) [0x7f2ebbe1b07e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x59) [0x7f2ebbe0cbdd] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::go(std::shared_ptr, std::shared_ptr)+0x70) [0x7f2ebbe1ad42] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosettaDNA.default.linuxgccdebug(+0xb7c1) [0x7f2ebe0b27c1] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosettaDNA.default.linuxgccdebug(+0xc079) [0x7f2ebe0b3079] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosettaDNA.default.linuxgccdebug(+0xb8d5) [0x7f2ebe0b28d5] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f2eb86040b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosettaDNA.default.linuxgccdebug(+0xb54e) [0x7f2ebe0b254e] [END_BACKTRACE] [FILE]: src/core/scoring/ScoreFunction.cc [LINE]: 468 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: bad line in file stage3.wts:fa_plane 0 [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2021.07+release.c48be26 [COMMIT_DATE]: 2021-02-22T05:58:26.229012 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug [MODE]: Debug [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm_new.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5e048c8b59] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xb2) [0x7f5e04927e4e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x76) [0x7f5e048cdf06] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x55) [0x7f5e048cd696] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::validate_template(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::shared_ptr, bool&)+0x3b7) [0x7f5e09048299] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::setup_templates_and_sampling_options(core::pose::Pose const&)+0x23a) [0x7f5e0904990a] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x54) [0x7f5e09049e2e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x340) [0x7f5e07416458] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x3f) [0x7f5e074160a1] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_debug::_Safe_iterator<__gnu_cxx::__normal_iterator > >, std::__debug::vector >, std::random_access_iterator_tag>)+0xa7) [0x7f5e0741745b] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x66b) [0x7f5e07410ec3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr&, long, std::__cxx11::basic_string, std::allocator >&, std::__cxx11::basic_string, std::allocator >&, unsigned long&, unsigned long&, bool)+0x1265) [0x7f5e06ef8089] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0xf6) [0x7f5e06ef607e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x59) [0x7f5e06ee7bdd] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x11af4) [0x7f5e09c33af4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f5e036e40b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1166e) [0x7f5e09c3366e] [END_BACKTRACE] [FILE]: src/protocols/hybridization/HybridizeProtocol.cc [LINE]: 903 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: Issue validating template in HybridizeProtocol. [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2021.07+release.c48be26 [COMMIT_DATE]: 2021-02-22T05:58:26.229012 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug [MODE]: Debug [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/database/ -in:file:fasta=Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm_new.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string, std::allocator > const&, int)+0x38) [0x7f149f3db8d0] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::save_crash_report(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, int)+0x38) [0x7f149f3d8d37] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(handle_assert_failure(char const*, std::__cxx11::basic_string, std::allocator > const&, int)+0x24d) [0x7f149f3d8056] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(utility::vectorL<1l, core::scoring::SmoothScoreTermCoeffs, std::allocator >::operator[](unsigned long) const+0x140) [0x7f148aceed3c] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(core::pose::Pose const&, core::conformation::Residue const&, numeric::xyzVector&, numeric::xyzVector&, numeric::xyzVector&) const+0xb91) [0x7f148aceca65] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.4.so(core::energy_methods::SmoothEnvEnergy::eval_residue_derivatives(core::conformation::Residue const&, core::scoring::ResSingleMinimizationData const&, core::pose::Pose const&, core::scoring::EMapVector const&, utility::vector1 >&) const+0x15c) [0x7f148e0fdea0] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::eval_atom_derivatives_for_minnode(core::scoring::MinimizationNode const&, core::conformation::Residue const&, core::pose::Pose const&, core::scoring::EMapVector const&, utility::vector1 >&)+0xdb) [0x7f148aaa8d10] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.5.so(core::optimization::cartesian_collect_atompairE_deriv(core::pose::Pose&, core::optimization::CartesianMinimizerMap&, core::scoring::ScoreFunction const&, utility::vector1 >&, double)+0x235) [0x7f148fa3538f] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.5.so(core::optimization::cartesian_dfunc(core::pose::Pose&, core::optimization::CartesianMinimizerMap&, core::scoring::ScoreFunction const&, utility::vector1 > const&, utility::vector1 >&)+0x194) [0x7f148fa350df] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.5.so(core::optimization::CartesianMultifunc::dfunc(utility::vector1 > const&, utility::vector1 >&) const+0x5d) [0x7f148fa6ff5b] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.5.so(core::optimization::Minimizer::run(utility::vector1 >&)+0x198) [0x7f148fa84b6a] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.5.so(core::optimization::CartesianMinimizer::run(core::pose::Pose&, core::kinematics::MoveMap const&, core::scoring::ScoreFunction const&, core::optimization::MinimizerOptions const&)+0x4e1) [0x7f148fa4b17f] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols_b.6.so(protocols::hybridization::CartesianHybridize::apply(core::pose::Pose&)+0x2b55) [0x7f14a3aba413] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x4143) [0x7f14a3b5df1d] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x340) [0x7f14a1f26458] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x3f) [0x7f14a1f260a1] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_debug::_Safe_iterator<__gnu_cxx::__normal_iterator > >, std::__debug::vector >, std::random_access_iterator_tag>)+0xa7) [0x7f14a1f2745b] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x66b) [0x7f14a1f20ec3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr&, long, std::__cxx11::basic_string, std::allocator >&, std::__cxx11::basic_string, std::allocator >&, unsigned long&, unsigned long&, bool)+0x1265) [0x7f14a1a08089] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0xf6) [0x7f14a1a0607e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x59) [0x7f14a19f7bdd] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x11af4) [0x7f14a4746af4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f149e1f40b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1166e) [0x7f14a474666e] [END_BACKTRACE] [FILE]: src/utility/vectorL.hh [LINE]: 420 [START_MESSAGE] ERROR: Assertion `static_cast< size_type >( i - l_ ) < super::size()` failed. ERROR:: Exit from: src/utility/vectorL.hh line: 420 [END_MESSAGE] [END_CRASH_REPORT] ############################################################################################################## # # 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]: 2021.07+release.c48be26 [COMMIT_DATE]: 2021-02-22T05:58:26.229012 [APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug [MODE]: Debug [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:path:database=/mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/database/ /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/database/ -in:file:fasta=Ca09HA.fasta Ca09HA.fasta -out:nstruct=1 -parser:protocol=rosetta_cm_new.xml -score:weights=stage3.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string, std::allocator > const&, int)+0x38) [0x7f26b1b6b8d0] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(utility::save_crash_report(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, int)+0x38) [0x7f26b1b68d37] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libutility.so(handle_assert_failure(char const*, std::__cxx11::basic_string, std::allocator > const&, int)+0x24d) [0x7f26b1b68056] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(utility::vectorL<1l, core::scoring::SmoothScoreTermCoeffs, std::allocator >::operator[](unsigned long) const+0x140) [0x7f269d47ed3c] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(core::pose::Pose const&, core::conformation::Residue const&, numeric::xyzVector&, numeric::xyzVector&, numeric::xyzVector&) const+0xb91) [0x7f269d47ca65] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.4.so(core::energy_methods::SmoothEnvEnergy::eval_residue_derivatives(core::conformation::Residue const&, core::scoring::ResSingleMinimizationData const&, core::pose::Pose const&, core::scoring::EMapVector const&, utility::vector1 >&) const+0x15c) [0x7f26a088dea0] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.3.so(core::scoring::eval_atom_derivatives_for_minnode(core::scoring::MinimizationNode const&, core::conformation::Residue const&, core::pose::Pose const&, core::scoring::EMapVector const&, utility::vector1 >&)+0xdb) [0x7f269d238d10] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.5.so(core::optimization::cartesian_collect_atompairE_deriv(core::pose::Pose&, core::optimization::CartesianMinimizerMap&, core::scoring::ScoreFunction const&, utility::vector1 >&, double)+0x235) [0x7f26a21c538f] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.5.so(core::optimization::cartesian_dfunc(core::pose::Pose&, core::optimization::CartesianMinimizerMap&, core::scoring::ScoreFunction const&, utility::vector1 > const&, utility::vector1 >&)+0x194) [0x7f26a21c50df] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.5.so(core::optimization::CartesianMultifunc::dfunc(utility::vector1 > const&, utility::vector1 >&) const+0x5d) [0x7f26a21fff5b] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.5.so(core::optimization::Minimizer::run(utility::vector1 >&)+0x198) [0x7f26a2214b6a] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libcore.5.so(core::optimization::CartesianMinimizer::run(core::pose::Pose&, core::kinematics::MoveMap const&, core::scoring::ScoreFunction const&, core::optimization::MinimizerOptions const&)+0x4e1) [0x7f26a21db17f] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols_b.6.so(protocols::hybridization::CartesianHybridize::apply(core::pose::Pose&)+0x2b55) [0x7f26b624a413] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x4143) [0x7f26b62edf1d] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x340) [0x7f26b46b6458] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x3f) [0x7f26b46b60a1] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_debug::_Safe_iterator<__gnu_cxx::__normal_iterator > >, std::__debug::vector >, std::random_access_iterator_tag>)+0xa7) [0x7f26b46b745b] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x66b) [0x7f26b46b0ec3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr&, long, std::__cxx11::basic_string, std::allocator >&, std::__cxx11::basic_string, std::allocator >&, unsigned long&, unsigned long&, bool)+0x1265) [0x7f26b4198089] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0xf6) [0x7f26b419607e] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/build/src/debug/linux/4.4/64/x86/gcc/9/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x59) [0x7f26b4187bdd] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x11af4) [0x7f26b6ed6af4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f26b09840b3] /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2021.07.61567_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug(+0x1166e) [0x7f26b6ed666e] [END_BACKTRACE] [FILE]: src/utility/vectorL.hh [LINE]: 420 [START_MESSAGE] ERROR: Assertion `static_cast< size_type >( i - l_ ) < super::size()` failed. ERROR:: Exit from: src/utility/vectorL.hh line: 420 [END_MESSAGE] [END_CRASH_REPORT]