############################################################################################################## # # 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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7f08b6a7c006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7f08b69e0d73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7f08b6a81a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7f08b6a817e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::components::StructureDataFactory::StructureDataFactory()+0x29c) [0x7f08a836303c] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0xd27) [0x7f08a8474cf7] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7f08b79f9796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7f08b7ce8e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7f08b7ce9840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7f08b7cecca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7f08b7e8f893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7f08b7e9157b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7f08b7e77ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x56280bf73457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f08b5d4ac87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x56280bf737da] [END_BACKTRACE] [FILE]: src/protocols/denovo_design/components/StructureDataFactory.cc [LINE]: 62 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: -run:preserve_header is required for using "Tomponents". To avoid this message, include "-run:preserve_header true" in your flags. [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7f08b6a7c006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7f08b69e0d73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7f08b6a81a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7f08b6a817e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::components::StructureDataFactory::StructureDataFactory()+0x29c) [0x7f08a836303c] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0xd27) [0x7f08a8474cf7] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7f08b79f9796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7f08b7ce8e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7f08b7ce9840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7f08b7cecca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7f08b7e8f893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7f08b7e9157b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7f08b7e77ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x56280bf73457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f08b5d4ac87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x56280bf737da] [END_BACKTRACE] [FILE]: src/protocols/denovo_design/components/StructureDataFactory.cc [LINE]: 62 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: -run:preserve_header is required for using "Tomponents". To avoid this message, include "-run:preserve_header true" in your flags. [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7f08b6a7c006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7f08b69e0d73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7f08b6a81a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7f08b6a817e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::components::StructureDataFactory::StructureDataFactory()+0x29c) [0x7f08a836303c] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0xd27) [0x7f08a8474cf7] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7f08b79f9796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7f08b7ce8e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7f08b7ce9840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7f08b7cecca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7f08b7e8f893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7f08b7e9157b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7f08b7e77ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x56280bf73457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f08b5d4ac87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x56280bf737da] [END_BACKTRACE] [FILE]: src/protocols/denovo_design/components/StructureDataFactory.cc [LINE]: 62 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: -run:preserve_header is required for using "Tomponents". To avoid this message, include "-run:preserve_header true" in your flags. [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7f08b6a7c006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7f08b69e0d73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7f08b6a81a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7f08b6a817e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::components::StructureDataFactory::StructureDataFactory()+0x29c) [0x7f08a836303c] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0xd27) [0x7f08a8474cf7] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7f08b79f9796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7f08b7ce8e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7f08b7ce9840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7f08b7cecca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7f08b7e8f893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7f08b7e9157b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7f08b7e77ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x56280bf73457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f08b5d4ac87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x56280bf737da] [END_BACKTRACE] [FILE]: src/protocols/denovo_design/components/StructureDataFactory.cc [LINE]: 62 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: -run:preserve_header is required for using "Tomponents". To avoid this message, include "-run:preserve_header true" in your flags. [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7f08b6a7c006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7f08b69e0d73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7f08b6a81a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7f08b6a817e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::components::StructureDataFactory::StructureDataFactory()+0x29c) [0x7f08a836303c] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0xd27) [0x7f08a8474cf7] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7f08b79f9796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7f08b7ce8e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7f08b7ce9840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7f08b7cecca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7f08b7e8f893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7f08b7e9157b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7f08b7e77ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x56280bf73457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f08b5d4ac87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x56280bf737da] [END_BACKTRACE] [FILE]: src/protocols/denovo_design/components/StructureDataFactory.cc [LINE]: 62 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: -run:preserve_header is required for using "Tomponents". To avoid this message, include "-run:preserve_header true" in your flags. [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7f08b6a7c006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7f08b69e0d73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7f08b6a81a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7f08b6a817e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::components::StructureDataFactory::StructureDataFactory()+0x29c) [0x7f08a836303c] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0xd27) [0x7f08a8474cf7] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7f08b79f9796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7f08b7ce8e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7f08b7ce9840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7f08b7cecca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7f08b7e8f893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7f08b7e9157b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7f08b7e77ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x56280bf73457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f08b5d4ac87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x56280bf737da] [END_BACKTRACE] [FILE]: src/protocols/denovo_design/components/StructureDataFactory.cc [LINE]: 62 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: -run:preserve_header is required for using "Tomponents". To avoid this message, include "-run:preserve_header true" in your flags. [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7f08b6a7c006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7f08b69e0d73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7f08b6a81a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7f08b6a817e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::components::StructureDataFactory::StructureDataFactory()+0x29c) [0x7f08a836303c] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0xd27) [0x7f08a8474cf7] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7f08b79f9796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7f08b7ce8e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7f08b7ce9840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7f08b7cecca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7f08b7e8f893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7f08b7e9157b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7f08b7e77ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x56280bf73457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f08b5d4ac87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x56280bf737da] [END_BACKTRACE] [FILE]: src/protocols/denovo_design/components/StructureDataFactory.cc [LINE]: 62 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: -run:preserve_header is required for using "Tomponents". To avoid this message, include "-run:preserve_header true" in your flags. [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -packing:dunbrack_prob_buried_semi=0.8 -packing:dunbrack_prob_nonburied_semi=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7f1408e9d006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7f1408e01d73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7f1408ea2a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7f1408ea27e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::components::StructureDataFactory::StructureDataFactory()+0x29c) [0x7f13fa78403c] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0xd27) [0x7f13fa895cf7] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7f1409e1a796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7f140a109e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7f140a10a840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7f140a10dca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7f140a2b0893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7f140a2b257b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7f140a298ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x557a31d7e457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f140816bc87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x557a31d7e7da] [END_BACKTRACE] [FILE]: src/protocols/denovo_design/components/StructureDataFactory.cc [LINE]: 62 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: -run:preserve_header is required for using "Tomponents". To avoid this message, include "-run:preserve_header true" in your flags. [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -packing:dunbrack_prob_buried_semi=0.8 -packing:dunbrack_prob_nonburied_semi=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7f1408e9d006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7f1408e01d73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7f1408ea2a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7f1408ea27e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::components::StructureDataFactory::StructureDataFactory()+0x29c) [0x7f13fa78403c] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0xd27) [0x7f13fa895cf7] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7f1409e1a796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7f140a109e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7f140a10a840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7f140a10dca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7f140a2b0893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7f140a2b257b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7f140a298ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x557a31d7e457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f140816bc87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x557a31d7e7da] [END_BACKTRACE] [FILE]: src/protocols/denovo_design/components/StructureDataFactory.cc [LINE]: 62 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: -run:preserve_header is required for using "Tomponents". To avoid this message, include "-run:preserve_header true" in your flags. [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -run:preserve_header -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -packing:dunbrack_prob_buried_semi=0.8 -packing:dunbrack_prob_nonburied_semi=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7fda3544b006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7fda353afd73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7fda35450a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7fda354507e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libcore.3.so(core::io::external::PsiPredInterface::run_psipred(core::pose::Pose const&, std::__cxx11::basic_string, std::allocator > const&)+0x2a76) [0x7fda2d0d51c6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0x576) [0x7fda26e43546] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7fda363c8796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7fda366b7e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7fda366b8840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7fda366bbca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7fda3685e893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7fda3686057b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7fda36846ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x55a008a06457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fda34719c87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x55a008a067da] [END_BACKTRACE] [FILE]: src/core/io/external/PsiPredInterface.cc [LINE]: 341 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: Failed to run the psipred command, which was "/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single SEDETIKKLV_HOPIEASN.fasta > /dev/null". Something went wrong. Make sure you specified the full path to the psipred command in your XML file. Return code=256 [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -run:preserve_header -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -packing:dunbrack_prob_buried_semi=0.8 -packing:dunbrack_prob_nonburied_semi=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7fda3544b006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7fda353afd73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7fda35450a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7fda354507e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libcore.3.so(core::io::external::PsiPredInterface::run_psipred(core::pose::Pose const&, std::__cxx11::basic_string, std::allocator > const&)+0x2a76) [0x7fda2d0d51c6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0x576) [0x7fda26e43546] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7fda363c8796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7fda366b7e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7fda366b8840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7fda366bbca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7fda3685e893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7fda3686057b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7fda36846ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x55a008a06457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fda34719c87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x55a008a067da] [END_BACKTRACE] [FILE]: src/core/io/external/PsiPredInterface.cc [LINE]: 341 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: Failed to run the psipred command, which was "/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single SEDETIKKLV_65I4RD77.fasta > /dev/null". Something went wrong. Make sure you specified the full path to the psipred command in your XML file. Return code=256 [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -run:preserve_header -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -packing:dunbrack_prob_buried_semi=0.8 -packing:dunbrack_prob_nonburied_semi=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7fda3544b006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7fda353afd73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7fda35450a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7fda354507e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libcore.3.so(core::io::external::PsiPredInterface::run_psipred(core::pose::Pose const&, std::__cxx11::basic_string, std::allocator > const&)+0x2a76) [0x7fda2d0d51c6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0x576) [0x7fda26e43546] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7fda363c8796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7fda366b7e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7fda366b8840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7fda366bbca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7fda3685e893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7fda3686057b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7fda36846ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x55a008a06457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fda34719c87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x55a008a067da] [END_BACKTRACE] [FILE]: src/core/io/external/PsiPredInterface.cc [LINE]: 341 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: Failed to run the psipred command, which was "/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single SEDETIKKLV_ZC38E0F0.fasta > /dev/null". Something went wrong. Make sure you specified the full path to the psipred command in your XML file. Return code=256 [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -run:preserve_header -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -packing:dunbrack_prob_buried_semi=0.8 -packing:dunbrack_prob_nonburied_semi=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7fda3544b006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7fda353afd73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7fda35450a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7fda354507e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libcore.3.so(core::io::external::PsiPredInterface::run_psipred(core::pose::Pose const&, std::__cxx11::basic_string, std::allocator > const&)+0x2a76) [0x7fda2d0d51c6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0x576) [0x7fda26e43546] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7fda363c8796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7fda366b7e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7fda366b8840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7fda366bbca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7fda3685e893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7fda3686057b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7fda36846ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x55a008a06457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fda34719c87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x55a008a067da] [END_BACKTRACE] [FILE]: src/core/io/external/PsiPredInterface.cc [LINE]: 341 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: Failed to run the psipred command, which was "/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single SEDETIKKLV_TQXAARO5.fasta > /dev/null". Something went wrong. Make sure you specified the full path to the psipred command in your XML file. Return code=256 [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -run:preserve_header -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -packing:dunbrack_prob_buried_semi=0.8 -packing:dunbrack_prob_nonburied_semi=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7feb4fcac006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7feb4fc10d73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7feb4fcb1a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7feb4fcb17e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libcore.3.so(core::io::external::PsiPredInterface::run_psipred(core::pose::Pose const&, std::__cxx11::basic_string, std::allocator > const&)+0x2a76) [0x7feb479361c6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0x576) [0x7feb416a4546] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7feb50c29796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7feb50f18e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7feb50f19840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7feb50f1cca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7feb510bf893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7feb510c157b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7feb510a7ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x56038de3e457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7feb4ef7ac87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x56038de3e7da] [END_BACKTRACE] [FILE]: src/core/io/external/PsiPredInterface.cc [LINE]: 341 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: Failed to run the psipred command, which was "/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single SEDETIKKLV_NE6E0ELT.fasta > /dev/null". Something went wrong. Make sure you specified the full path to the psipred command in your XML file. Return code=256 [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]: 2022.41+release.28dc2a1 [COMMIT_DATE]: 2022-10-15T22:48:55.778002 [APPLICATION]: /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "7.5.0" [STDLIB]: libstdc++ version 20191114 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/3DI/rifdock_out_splits/xae.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:score_only=score.sc -run:preserve_header -parser:protocol=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol/paper_predictor.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/shanghai/RationalDesign/Rosetta3.9/2022-nature-CaoLX/scripts_and_main_pdbs/cao_2021_protocol patchdock_res=176,177,123,66,65,64 runpsipred_single=/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single -packing:dunbrack_prob_buried=0.8 -packing:dunbrack_prob_nonburied=0.8 -packing:dunbrack_prob_buried_semi=0.8 -packing:dunbrack_prob_nonburied_semi=0.8 -corrections:beta_nov16 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7feb4fcac006] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xe3) [0x7feb4fc10d73] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x10f) [0x7feb4fcb1a2f] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x7feb4fcb17e6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libcore.3.so(core::io::external::PsiPredInterface::run_psipred(core::pose::Pose const&, std::__cxx11::basic_string, std::allocator > const&)+0x2a76) [0x7feb479361c6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::filters::SSPredictionFilter::compute(core::pose::Pose const&) const+0x576) [0x7feb416a4546] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::filters::MoveBeforeFilter::report_sm(core::pose::Pose const&) const+0x46) [0x7feb50c29796] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(core::pose::Pose&) const+0x2d9) [0x7feb50f18e89] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::finish_protocol(core::pose::Pose&)+0x70) [0x7feb50f19840] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2c6) [0x7feb50f1cca6] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/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)+0xd73) [0x7feb510bf893] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x1bb) [0x7feb510c157b] /home/shanghai/RationalDesign/rosetta/main/source/build/src/release/linux/5.3/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x56) [0x7feb510a7ea6] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x4457) [0x56038de3e457] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7feb4ef7ac87] /home/shanghai/RationalDesign/rosetta/main/source/bin/rosetta_scripts.linuxgccrelease(+0x47da) [0x56038de3e7da] [END_BACKTRACE] [FILE]: src/core/io/external/PsiPredInterface.cc [LINE]: 341 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: Failed to run the psipred command, which was "/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single SEDETIKKLV_RCR6QVHC.fasta > /dev/null". Something went wrong. Make sure you specified the full path to the psipred command in your XML file. Return code=256 [END_MESSAGE] [END_CRASH_REPORT]