##############################################################################################################
#
# 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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[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]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:57:38.289184
[APPLICATION]: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease
[MODE]: Release
[EXTRAS]: hdf5 
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
 -in:file:keep_input_scores=false -in:file:silent=/home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/pilot_splits/xau.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/gaon/cao_protocol/cao_2021_protocol/paper_interface_design.xml -parser:script_vars=CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol patchdock_res=51,53,55,76,79,80,82,85,87 runpsipred_single=/home/gaon/biosoftware/psipred/runpsipred_single -corrections:beta_nov16 -holes:dalphaball=/home/gaon/biosoftware/rosetta39/main/source/external/DAlpahBall -indexed_structure_store:fragment_store=/home/gaon/cao_protocol/ss_grouped_vall_all.h5

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5ca61a99da]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5ca61e6fb0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5ca61ae303]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5ca61adf4b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::packing::get_surf_vol(core::pose::Pose const&, core::id::AtomID_Map<bool> const&, double)+0x33c0) [0x7f5c9eeb2860]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::sap_atom_sasa(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0xbd0) [0x7f5ca06239b0]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa()+0x1022) [0x7f5ca061a9f2]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapDatabase::SapDatabase()+0x9b) [0x7f5ca061b66b]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::init()+0x2bf) [0x7f5ca05fd1ef]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions const> const&)+0x7ef) [0x7f5ca05fdaff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::common_setup(std::shared_ptr<core::pack::guidance_scoreterms::sap::SapConstraintOptions> const&, core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, utility::vector1<std::shared_ptr<core::conformation::Residue const>, std::allocator<std::shared_ptr<core::conformation::Residue const> > >&)+0xf6) [0x7f5ca06277e6]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::calculate_sap(core::pose::Pose const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&, std::shared_ptr<core::select::residue_selector::ResidueSelector const> const&)+0xd5) [0x7f5ca0627aa5]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(core::pose::Pose const&) const+0xcf) [0x7f5ca061d8ff]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libcore.3.so(core::simple_metrics::RealMetric::apply(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::pose::Pose&, bool) const+0x39) [0x7f5c9dece539]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_metrics(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x7e) [0x7f5ca77553de]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x8e) [0x7f5ca7757d3e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x7f5ca7758330]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x20e) [0x7f5ca775a34e]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe58) [0x7f5ca7301048]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f5ca7302fb8]
/home/gaon/biosoftware/rosetta313/main/source/build/src/release/linux/6.2/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f5ca72eb919]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4ab5) [0x55f1ed349ab5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5ca5829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5ca5829e40]
/home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease(+0x4d85) [0x55f1ed349d85]

[END_BACKTRACE]

[FILE]: src/core/scoring/packing/surf_vol.cc
[LINE]: 170
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: 



[END_MESSAGE]
[END_CRASH_REPORT]