############################################################################################################## # # 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]: 2022.12+release.a4d7970 [COMMIT_DATE]: 2022-03-22T15:27:26.590656 [APPLICATION]: /home/newdisk1/rosetta.binary.linux.release-315/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease [MODE]: Release [EXTRAS]: hdf5 [OS]: GNU/Linux [COMPILER]: GCC version "9.4.0" [STDLIB]: libstdc++ version 20210601 [START_OPTIONS] -in:file:keep_input_scores=false -in:file:silent=/home/newdisk1/binder_design/pilot_splits/xah.silent -in:file:silent_read_through_errors -out:mute=protocols.rosetta_scripts.ParsedProtocol.REPORT -out:file:silent=out.silent -out:file:silent_struct_type=binary -parser:protocol=/home/zhengjishen/Desktop/caolongxing_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/zhengjishen/Desktop/caolongxing_protocol/cao_2021_protocol patchdock_res=4,5,8,12,13 runpsipred_single=/home/zhengjishen/Desktop/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 -holes:dalphaball=/home/newdisk1/rosetta.binary.linux.release-315/main/source/external/DAlphaBall -indexed_structure_store:fragment_store=/home/zhengjishen/Desktop/ss_grouped_vall_all.h5 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7fe17ca218aa] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x103) [0x7fe17c96bd83] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x113) [0x7fe17ca266a3] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x3b) [0x7fe17ca2646b] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map const&, double)+0x38ac) [0x7fe1760aff4c] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1 > const&)+0x885) [0x7fe17754b715] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0xf92) [0x7fe17753e5b2] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7fe17753f33b] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2c7) [0x7fe17751d2e7] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr const&)+0x849) [0x7fe17751dc99] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr const&, core::pose::Pose const&, std::shared_ptr const&, std::shared_ptr const&, std::shared_ptr const&, utility::vector1, std::allocator > >&)+0xe3) [0x7fe17754f903] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr const&, std::shared_ptr const&, std::shared_ptr const&, core::pack::guidance_scoreterms::sap::SapParameterOptions const&)+0xee) [0x7fe17754fbde] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xbe) [0x7fe177540c3e] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string, std::allocator > const&, core::pose::Pose&, bool) const+0x3b) [0x7fe17603d0eb] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x81) [0x7fe17d982c01] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7fe17d985bfe] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator > >)+0x40) [0x7fe17d9863b0] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x2be) [0x7fe17d98a94e] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/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)+0x22b4) [0x7fe17db25344] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x238) [0x7fe17db268b8] /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x57) [0x7fe17db0e367] /home/newdisk1/rosetta.binary.linux.release-315/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4a96) [0x55f78337aa96] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7fe17c2d00b3] /home/newdisk1/rosetta.binary.linux.release-315/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d3e) [0x55f78337ad3e] [END_BACKTRACE] [FILE]: src/core/scoring/packing/surf_vol.cc [LINE]: 164 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: [END_MESSAGE] [END_CRASH_REPORT]