##############################################################################################################
#
# 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]: 2023.24+release.9fbc647
[COMMIT_DATE]: 2023-06-12T21:00:29.174178
[APPLICATION]: UNKNOWN APPLICATION
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: Clang version "14.0.0 "
[STDLIB]: libstdc++ version 20220421
[START_OPTIONS]
NO OPTIONS SPECIFIED

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(backtrace_string[abi:cxx11](int)+0x3d) [0x7fb9d40ea9fd]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x125) [0x7fb9d41090e5]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::options::OptionCollection::load_options_from_file_exception(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x1d2) [0x7fb9d41db212]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::options::OptionCollection::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::list<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, bool)+0x40f) [0x7fb9d41d51bf]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::options::OptionCollection::load(int, char* const*, bool)+0x222) [0x7fb9d41d6412]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libcore.6.so(core::init::init(int, char**)+0x29) [0x7fb9d7c72299]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x3710) [0x7fb9de592710]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7fb9d2d29d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7fb9d2d29e40]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x34f5) [0x7fb9de5924f5]

[END_BACKTRACE]

[FILE]: src/utility/options/OptionCollection.cc
[LINE]: 572
[START_MESSAGE]
Option file open failed for: 'rosetta_cm.opitions'

[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]: 2023.24+release.9fbc647
[COMMIT_DATE]: 2023-06-12T21:00:29.174178
[APPLICATION]: /home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: Clang version "14.0.0 "
[STDLIB]: libstdc++ version 20220421
[START_OPTIONS]
 -in:file:fasta=dkmm.fasta -out:nstruct=3 -parser:protocol=rosetta_cm.xml -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(backtrace_string[abi:cxx11](int)+0x3d) [0x7f682085a9fd]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x125) [0x7f68208790e5]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xb3) [0x7f682085df53]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x31) [0x7f682085de31]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libcore.6.so(core::fragment::chop_fragments(core::fragment::FragSet&, core::fragment::FragSet&)+0x6bc) [0x7f68242e9c0c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize(unsigned long, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > > const&, utility::vector1<double, std::allocator<double> > const&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> > const&, std::shared_ptr<core::fragment::FragSet>, std::shared_ptr<core::fragment::FragSet>)+0xa9c) [0x7f6828c28d5c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(void __gnu_cxx::new_allocator<protocols::hybridization::FoldTreeHybridize>::construct<protocols::hybridization::FoldTreeHybridize, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&>(protocols::hybridization::FoldTreeHybridize*, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&)+0x90) [0x7f6828c94ac0]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x4590) [0x7f6828c6c350]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x554) [0x7f6824c22fb4]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0xb50) [0x7f6824c1bc80]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/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)+0x2067) [0x7f68248e8547]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xdc) [0x7f68248e543c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x53) [0x7f68248dfd33]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x3e0a) [0x7f682acfce0a]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f681f499d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f681f499e40]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x34f5) [0x7f682acfc4f5]

[END_BACKTRACE]

[FILE]: src/core/fragment/util.cc
[LINE]: 177
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `tlen < slen` failed.



[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]: 2023.24+release.9fbc647
[COMMIT_DATE]: 2023-06-12T21:00:29.174178
[APPLICATION]: /home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: Clang version "14.0.0 "
[STDLIB]: libstdc++ version 20220421
[START_OPTIONS]
 -in:file:fasta=dkmm.fasta -out:nstruct=3 -parser:protocol=rosetta_cm.xml -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(backtrace_string[abi:cxx11](int)+0x3d) [0x7f682085a9fd]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x125) [0x7f68208790e5]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xb3) [0x7f682085df53]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x31) [0x7f682085de31]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libcore.6.so(core::fragment::chop_fragments(core::fragment::FragSet&, core::fragment::FragSet&)+0x6bc) [0x7f68242e9c0c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize(unsigned long, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > > const&, utility::vector1<double, std::allocator<double> > const&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> > const&, std::shared_ptr<core::fragment::FragSet>, std::shared_ptr<core::fragment::FragSet>)+0xa9c) [0x7f6828c28d5c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(void __gnu_cxx::new_allocator<protocols::hybridization::FoldTreeHybridize>::construct<protocols::hybridization::FoldTreeHybridize, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&>(protocols::hybridization::FoldTreeHybridize*, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&)+0x90) [0x7f6828c94ac0]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x4590) [0x7f6828c6c350]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x554) [0x7f6824c22fb4]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0xb50) [0x7f6824c1bc80]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/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)+0x2067) [0x7f68248e8547]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xdc) [0x7f68248e543c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x53) [0x7f68248dfd33]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x3e0a) [0x7f682acfce0a]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f681f499d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f681f499e40]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x34f5) [0x7f682acfc4f5]

[END_BACKTRACE]

[FILE]: src/core/fragment/util.cc
[LINE]: 177
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `tlen < slen` failed.



[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]: 2023.24+release.9fbc647
[COMMIT_DATE]: 2023-06-12T21:00:29.174178
[APPLICATION]: /home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: Clang version "14.0.0 "
[STDLIB]: libstdc++ version 20220421
[START_OPTIONS]
 -in:file:fasta=dkmm.fasta -out:nstruct=3 -parser:protocol=rosetta_cm.xml -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(backtrace_string[abi:cxx11](int)+0x3d) [0x7f682085a9fd]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x125) [0x7f68208790e5]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xb3) [0x7f682085df53]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x31) [0x7f682085de31]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libcore.6.so(core::fragment::chop_fragments(core::fragment::FragSet&, core::fragment::FragSet&)+0x6bc) [0x7f68242e9c0c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize(unsigned long, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > > const&, utility::vector1<double, std::allocator<double> > const&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> > const&, std::shared_ptr<core::fragment::FragSet>, std::shared_ptr<core::fragment::FragSet>)+0xa9c) [0x7f6828c28d5c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(void __gnu_cxx::new_allocator<protocols::hybridization::FoldTreeHybridize>::construct<protocols::hybridization::FoldTreeHybridize, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&>(protocols::hybridization::FoldTreeHybridize*, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&)+0x90) [0x7f6828c94ac0]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x4590) [0x7f6828c6c350]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x554) [0x7f6824c22fb4]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0xb50) [0x7f6824c1bc80]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/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)+0x2067) [0x7f68248e8547]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xdc) [0x7f68248e543c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x53) [0x7f68248dfd33]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x3e0a) [0x7f682acfce0a]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f681f499d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f681f499e40]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x34f5) [0x7f682acfc4f5]

[END_BACKTRACE]

[FILE]: src/core/fragment/util.cc
[LINE]: 177
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `tlen < slen` failed.



[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]: 2023.24+release.9fbc647
[COMMIT_DATE]: 2023-06-12T21:00:29.174178
[APPLICATION]: /home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: Clang version "14.0.0 "
[STDLIB]: libstdc++ version 20220421
[START_OPTIONS]
 -in:file:fasta=dkmm.fasta -out:nstruct=3 -parser:protocol=rosetta_cm.xml -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(backtrace_string[abi:cxx11](int)+0x3d) [0x7f153daba9fd]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x125) [0x7f153dad90e5]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xb3) [0x7f153dabdf53]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x31) [0x7f153dabde31]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libcore.6.so(core::fragment::chop_fragments(core::fragment::FragSet&, core::fragment::FragSet&)+0x6bc) [0x7f1541549c0c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize(unsigned long, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > > const&, utility::vector1<double, std::allocator<double> > const&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> > const&, std::shared_ptr<core::fragment::FragSet>, std::shared_ptr<core::fragment::FragSet>)+0xa9c) [0x7f1545e88d5c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(void __gnu_cxx::new_allocator<protocols::hybridization::FoldTreeHybridize>::construct<protocols::hybridization::FoldTreeHybridize, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&>(protocols::hybridization::FoldTreeHybridize*, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&)+0x90) [0x7f1545ef4ac0]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x4590) [0x7f1545ecc350]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x554) [0x7f1541e82fb4]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0xb50) [0x7f1541e7bc80]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/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)+0x2067) [0x7f1541b48547]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xdc) [0x7f1541b4543c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x53) [0x7f1541b3fd33]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x3e0a) [0x7f1547f5fe0a]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f153c6f9d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f153c6f9e40]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x34f5) [0x7f1547f5f4f5]

[END_BACKTRACE]

[FILE]: src/core/fragment/util.cc
[LINE]: 177
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `tlen < slen` failed.



[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]: 2023.24+release.9fbc647
[COMMIT_DATE]: 2023-06-12T21:00:29.174178
[APPLICATION]: /home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: Clang version "14.0.0 "
[STDLIB]: libstdc++ version 20220421
[START_OPTIONS]
 -in:file:fasta=dkmm.fasta -out:nstruct=3 -parser:protocol=rosetta_cm.xml -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(backtrace_string[abi:cxx11](int)+0x3d) [0x7f153daba9fd]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x125) [0x7f153dad90e5]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xb3) [0x7f153dabdf53]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x31) [0x7f153dabde31]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libcore.6.so(core::fragment::chop_fragments(core::fragment::FragSet&, core::fragment::FragSet&)+0x6bc) [0x7f1541549c0c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize(unsigned long, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > > const&, utility::vector1<double, std::allocator<double> > const&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> > const&, std::shared_ptr<core::fragment::FragSet>, std::shared_ptr<core::fragment::FragSet>)+0xa9c) [0x7f1545e88d5c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(void __gnu_cxx::new_allocator<protocols::hybridization::FoldTreeHybridize>::construct<protocols::hybridization::FoldTreeHybridize, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&>(protocols::hybridization::FoldTreeHybridize*, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&)+0x90) [0x7f1545ef4ac0]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x4590) [0x7f1545ecc350]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x554) [0x7f1541e82fb4]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0xb50) [0x7f1541e7bc80]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/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)+0x2067) [0x7f1541b48547]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xdc) [0x7f1541b4543c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x53) [0x7f1541b3fd33]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x3e0a) [0x7f1547f5fe0a]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f153c6f9d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f153c6f9e40]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x34f5) [0x7f1547f5f4f5]

[END_BACKTRACE]

[FILE]: src/core/fragment/util.cc
[LINE]: 177
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `tlen < slen` failed.



[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]: 2023.24+release.9fbc647
[COMMIT_DATE]: 2023-06-12T21:00:29.174178
[APPLICATION]: /home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: Clang version "14.0.0 "
[STDLIB]: libstdc++ version 20220421
[START_OPTIONS]
 -in:file:fasta=dkmm.fasta -out:nstruct=3 -parser:protocol=rosetta_cm.xml -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(backtrace_string[abi:cxx11](int)+0x3d) [0x7f153daba9fd]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x125) [0x7f153dad90e5]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xb3) [0x7f153dabdf53]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x31) [0x7f153dabde31]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libcore.6.so(core::fragment::chop_fragments(core::fragment::FragSet&, core::fragment::FragSet&)+0x6bc) [0x7f1541549c0c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize(unsigned long, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > > const&, utility::vector1<double, std::allocator<double> > const&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> > const&, std::shared_ptr<core::fragment::FragSet>, std::shared_ptr<core::fragment::FragSet>)+0xa9c) [0x7f1545e88d5c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(void __gnu_cxx::new_allocator<protocols::hybridization::FoldTreeHybridize>::construct<protocols::hybridization::FoldTreeHybridize, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&>(protocols::hybridization::FoldTreeHybridize*, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&)+0x90) [0x7f1545ef4ac0]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x4590) [0x7f1545ecc350]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x554) [0x7f1541e82fb4]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0xb50) [0x7f1541e7bc80]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/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)+0x2067) [0x7f1541b48547]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xdc) [0x7f1541b4543c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x53) [0x7f1541b3fd33]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x3e0a) [0x7f1547f5fe0a]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f153c6f9d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f153c6f9e40]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x34f5) [0x7f1547f5f4f5]

[END_BACKTRACE]

[FILE]: src/core/fragment/util.cc
[LINE]: 177
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `tlen < slen` failed.



[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]: 2023.24+release.9fbc647
[COMMIT_DATE]: 2023-06-12T21:00:29.174178
[APPLICATION]: /home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: Clang version "14.0.0 "
[STDLIB]: libstdc++ version 20220421
[START_OPTIONS]
 -in:file:fasta=dkmm.fasta -out:nstruct=3 -parser:protocol=rosetta_cm.xml -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(backtrace_string[abi:cxx11](int)+0x3d) [0x7f488ad1a9fd]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x125) [0x7f488ad390e5]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xb3) [0x7f488ad1df53]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x31) [0x7f488ad1de31]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libcore.6.so(core::fragment::chop_fragments(core::fragment::FragSet&, core::fragment::FragSet&)+0x6bc) [0x7f488e7a9c0c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize(unsigned long, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > > const&, utility::vector1<double, std::allocator<double> > const&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> > const&, std::shared_ptr<core::fragment::FragSet>, std::shared_ptr<core::fragment::FragSet>)+0xa9c) [0x7f48930e8d5c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(void __gnu_cxx::new_allocator<protocols::hybridization::FoldTreeHybridize>::construct<protocols::hybridization::FoldTreeHybridize, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&>(protocols::hybridization::FoldTreeHybridize*, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&)+0x90) [0x7f4893154ac0]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x4590) [0x7f489312c350]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x554) [0x7f488f0e2fb4]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0xb50) [0x7f488f0dbc80]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/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)+0x2067) [0x7f488eda8547]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xdc) [0x7f488eda543c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x53) [0x7f488ed9fd33]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x3e0a) [0x7f48951b7e0a]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f4889959d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f4889959e40]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x34f5) [0x7f48951b74f5]

[END_BACKTRACE]

[FILE]: src/core/fragment/util.cc
[LINE]: 177
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `tlen < slen` failed.



[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]: 2023.24+release.9fbc647
[COMMIT_DATE]: 2023-06-12T21:00:29.174178
[APPLICATION]: /home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: Clang version "14.0.0 "
[STDLIB]: libstdc++ version 20220421
[START_OPTIONS]
 -in:file:fasta=dkmm.fasta -out:nstruct=3 -parser:protocol=rosetta_cm.xml -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(backtrace_string[abi:cxx11](int)+0x3d) [0x7f488ad1a9fd]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x125) [0x7f488ad390e5]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xb3) [0x7f488ad1df53]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x31) [0x7f488ad1de31]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libcore.6.so(core::fragment::chop_fragments(core::fragment::FragSet&, core::fragment::FragSet&)+0x6bc) [0x7f488e7a9c0c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize(unsigned long, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > > const&, utility::vector1<double, std::allocator<double> > const&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> > const&, std::shared_ptr<core::fragment::FragSet>, std::shared_ptr<core::fragment::FragSet>)+0xa9c) [0x7f48930e8d5c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(void __gnu_cxx::new_allocator<protocols::hybridization::FoldTreeHybridize>::construct<protocols::hybridization::FoldTreeHybridize, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&>(protocols::hybridization::FoldTreeHybridize*, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&)+0x90) [0x7f4893154ac0]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x4590) [0x7f489312c350]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x554) [0x7f488f0e2fb4]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0xb50) [0x7f488f0dbc80]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/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)+0x2067) [0x7f488eda8547]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xdc) [0x7f488eda543c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x53) [0x7f488ed9fd33]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x3e0a) [0x7f48951b7e0a]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f4889959d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f4889959e40]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x34f5) [0x7f48951b74f5]

[END_BACKTRACE]

[FILE]: src/core/fragment/util.cc
[LINE]: 177
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `tlen < slen` failed.



[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]: 2023.24+release.9fbc647
[COMMIT_DATE]: 2023-06-12T21:00:29.174178
[APPLICATION]: /home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: Clang version "14.0.0 "
[STDLIB]: libstdc++ version 20220421
[START_OPTIONS]
 -in:file:fasta=dkmm.fasta -out:nstruct=3 -parser:protocol=rosetta_cm.xml -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(backtrace_string[abi:cxx11](int)+0x3d) [0x7f488ad1a9fd]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x125) [0x7f488ad390e5]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xb3) [0x7f488ad1df53]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x31) [0x7f488ad1de31]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libcore.6.so(core::fragment::chop_fragments(core::fragment::FragSet&, core::fragment::FragSet&)+0x6bc) [0x7f488e7a9c0c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize(unsigned long, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > > const&, utility::vector1<double, std::allocator<double> > const&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> > const&, std::shared_ptr<core::fragment::FragSet>, std::shared_ptr<core::fragment::FragSet>)+0xa9c) [0x7f48930e8d5c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(void __gnu_cxx::new_allocator<protocols::hybridization::FoldTreeHybridize>::construct<protocols::hybridization::FoldTreeHybridize, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&>(protocols::hybridization::FoldTreeHybridize*, unsigned long&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&, utility::vector1<double, std::allocator<double> >&, utility::vector1<protocols::loops::Loops, std::allocator<protocols::loops::Loops> >&, std::shared_ptr<core::fragment::FragSet>&, std::shared_ptr<core::fragment::FragSet>&)+0x90) [0x7f4893154ac0]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols_b.6.so(protocols::hybridization::HybridizeProtocol::apply(core::pose::Pose&)+0x4590) [0x7f489312c350]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x554) [0x7f488f0e2fb4]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0xb50) [0x7f488f0dbc80]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/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)+0x2067) [0x7f488eda8547]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xdc) [0x7f488eda543c]
/home/user/Rosetta/main/source/build/src/release/linux/4.4/64/x86/clang/14.0/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x53) [0x7f488ed9fd33]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x3e0a) [0x7f48951b7e0a]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f4889959d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f4889959e40]
/home/user/Rosetta/main/source/bin/rosetta_scripts.default.linuxclangrelease(+0x34f5) [0x7f48951b74f5]

[END_BACKTRACE]

[FILE]: src/core/fragment/util.cc
[LINE]: 177
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `tlen < slen` failed.



[END_MESSAGE]
[END_CRASH_REPORT]