############################################################################################################## # # Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/ # or use the script Rosetta/main/source/scripts/python/public/report_crashes.py # [START_CRASH_REPORT] [ROSETTA_VERSION]: 2020.50+release.1295438 [COMMIT_DATE]: 2020-12-13T21:33:15.479874 [APPLICATION]: /home/progs/rosetta_src_2020.50.61505_bundle/main/source//bin/cluster.linuxgccrelease [MODE]: Release [EXTRAS]: default [OS]: GNU/Linux [COMPILER]: GCC version "5.4.0 20160609" [STDLIB]: libstdc++ version 20160609 [START_OPTIONS] -in:path:database=/home/progs/rosetta_src_2020.50.61505_bundle/main/database/ -in:file:l=pdb_list.txt -out:prefix=clustered -out:path:all=output/ -run:chain=A -cluster:exclude_res=332 -cluster:radius=-1 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x2b9292734ec6] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0xf2) [0x2b9292777542] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x110) [0x2b929273a0f0] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x36) [0x2b9292739dc6] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::__cxx11::basic_string, std::allocator > const&, utility::vector1, std::allocator > > const&)+0x4d5) [0x2b928f5de585] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::__cxx11::basic_string, std::allocator > const&, bool&)+0x1e7) [0x2b928f5ef607] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types()+0x733) [0x2b928f5f0c53] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(core::io::StructFileRep const&, core::pose::Pose&)+0xbc) [0x2b928f5f2eec] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libcore.6.so(core::import_pose::build_pose_as_is(std::shared_ptr, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0xe3) [0x2b928e9b3613] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libcore.6.so(core::import_pose::build_pose(std::shared_ptr, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0x9e) [0x2b928e9b37fe] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libcore.6.so(core::import_pose::pose_from_file(core::pose::Pose&, core::chemical::ResidueTypeSet const&, std::__cxx11::basic_string, std::allocator > const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x866) [0x2b928e9b41e6] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libcore.6.so(core::import_pose::pose_from_file(core::pose::Pose&, core::chemical::ResidueTypeSet const&, std::__cxx11::basic_string, std::allocator > const&, bool, core::import_pose::FileType)+0x56) [0x2b928e9b45c6] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libcore.6.so(core::import_pose::pose_stream::PDBPoseInputStream::fill_pose(core::pose::Pose&, core::chemical::ResidueTypeSet const&, bool)+0x375) [0x2b928eace185] /home/progs/rosetta_src_2020.50.61505_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libcore.6.so(core::import_pose::pose_stream::MetaPoseInputStream::fill_pose(core::pose::Pose&, core::chemical::ResidueTypeSet const&, bool)+0x224) [0x2b928eac5704] /home/progs/rosetta_src_2020.50.61505_bundle/main/source//bin/cluster.linuxgccrelease() [0x408ac7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x2b92933be840] /home/progs/rosetta_src_2020.50.61505_bundle/main/source//bin/cluster.linuxgccrelease() [0x409269] [END_BACKTRACE] [FILE]: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc [LINE]: 1439 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: Unrecognized residue: lig [END_MESSAGE] [END_CRASH_REPORT]