==225604== Memcheck, a memory error detector
==225604== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==225604== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
==225604== Command: /home/shuhao/Downloads/rifdock/build/apps/rosetta/rifgen @input/rifgen.flag
==225604== 
core.init: Rosetta version: rosetta.binary.linux.release-171 r171 2018.09+release.333d996 333d99699777cd6a50d1c1736bacd689f8f1d1df https://www.rosettacommons.org 2018-02-27T09:57:00.705373
core.init: command: /home/shuhao/Downloads/rifdock/build/apps/rosetta/rifgen @input/rifgen.flag
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1308852539 seed_offset=0 real_seed=1308852539
core.init.random: RandomGenerator:init: Normal mode, seed=1308852539 RG_type=mt19937
Rifdock thinks there are 8 threads.
rif_type: RotScore64

=================================================== preparing target ===================================================

basic.io.database: [ WARNING ] Unable to locate database file chemical/residue_type_sets/fa_standard
core.chemical.GlobalResidueTypeSet: For ResidueTypeSet fa_standard there is no exclude_pdb_component_list.txt file to list known PDB ids.
core.chemical.GlobalResidueTypeSet:     This will turn off PDB component loading for ResidueTypeSet fa_standard
core.chemical.GlobalResidueTypeSet:     Expected file: /home/me/rifdock/rifdock_rosetta/main/database/chemical/residue_type_sets/fa_standard/exclude_pdb_component_list.txt

ERROR: Unable to open file: /home/me/rifdock/rifdock_rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types.txt

ERROR:: Exit from: /home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/core/chemical/GlobalResidueTypeSet.cc line: 144
BACKTRACE:
/home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x2ea) [0x85a522a]
/home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::GlobalResidueTypeSet::init_restypes_from_database()+0xe48) [0x52ad558]
/home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::GlobalResidueTypeSet::GlobalResidueTypeSet(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&)+0x1b6) [0x52bb6a6]
/home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::ChemicalManager::create_residue_type_set(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const+0x21a) [0x5289e6a]
/home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so(boost::detail::function::function_obj_invoker0<boost::_bi::bind_t<std::shared_ptr<core::chemical::GlobalResidueTypeSet>, boost::_mfi::cmf1<std::shared_ptr<core::chemical::GlobalResidueTypeSet>, core::chemical::ChemicalManager, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>, boost::_bi::list2<boost::_bi::value<core::chemical::ChemicalManager*>, boost::reference_wrapper<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const> > >, std::shared_ptr<core::chemical::GlobalResidueTypeSet> >::invoke(boost::detail::function::function_buffer&)+0x3e) [0x5290f1e]
/home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::ChemicalManager::residue_type_set(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x2df) [0x528e06f]
/home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so(core::chemical::ChemicalManager::residue_type_set(core::chemical::TypeSetMode)+0x39) [0x528e819]
/home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so(core::conformation::Conformation::residue_type_set_for_conf(core::chemical::TypeSetMode) const+0xca) [0x517ae5a]
/home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.3.so(core::pose::Pose::residue_type_set_for_pose(core::chemical::TypeSetMode) const+0x21) [0x600d061]
/home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x9d) [0x7fb025d]
/home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, core::import_pose::FileType)+0x4d) [0x7fb035d]
/home/shuhao/Downloads/rifdock/build/apps/rosetta/rifgen(main+0x7d4) [0x431114]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x9075083]
/home/shuhao/Downloads/rifdock/build/apps/rosetta/rifgen(_start+0x2e) [0x43967e]
terminate called after throwing an instance of 'utility::UtilityExitException'
  what():  

File: /home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/core/chemical/GlobalResidueTypeSet.cc:144
[ ERROR ] UtilityExitException
ERROR: Unable to open file: /home/me/rifdock/rifdock_rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types.txt



==225604== 
==225604== Process terminating with default action of signal 6 (SIGABRT)
==225604==    at 0x909400B: raise (raise.c:51)
==225604==    by 0x9073858: abort (abort.c:79)
==225604==    by 0x8D80910: ??? (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28)
==225604==    by 0x8D8C38B: ??? (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28)
==225604==    by 0x8D8C3F6: std::terminate() (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28)
==225604==    by 0x8D8C6A8: __cxa_throw (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28)
==225604==    by 0x85A5BFA: utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int) (in /home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libutility.so)
==225604==    by 0x52AD557: core::chemical::GlobalResidueTypeSet::init_restypes_from_database() (in /home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so)
==225604==    by 0x52BB6A5: core::chemical::GlobalResidueTypeSet::GlobalResidueTypeSet(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&) (in /home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so)
==225604==    by 0x5289E69: core::chemical::ChemicalManager::create_residue_type_set(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const (in /home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so)
==225604==    by 0x5290F1D: boost::detail::function::function_obj_invoker0<boost::_bi::bind_t<std::shared_ptr<core::chemical::GlobalResidueTypeSet>, boost::_mfi::cmf1<std::shared_ptr<core::chemical::GlobalResidueTypeSet>, core::chemical::ChemicalManager, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>, boost::_bi::list2<boost::_bi::value<core::chemical::ChemicalManager*>, boost::reference_wrapper<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const> > >, std::shared_ptr<core::chemical::GlobalResidueTypeSet> >::invoke(boost::detail::function::function_buffer&) (in /home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so)
==225604==    by 0x528E06E: core::chemical::ChemicalManager::residue_type_set(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) (in /home/shuhao/Downloads/rosetta_bin_linux_2018.09.60072_bundle/main/source/cmake/build_cxx11_omp/libcore.2.so)
==225604== 
==225604== HEAP SUMMARY:
==225604==     in use at exit: 7,574,557 bytes in 71,030 blocks
==225604==   total heap usage: 241,929 allocs, 170,899 frees, 16,325,771 bytes allocated
==225604== 
==225604== LEAK SUMMARY:
==225604==    definitely lost: 0 bytes in 0 blocks
==225604==    indirectly lost: 0 bytes in 0 blocks
==225604==      possibly lost: 168 bytes in 1 blocks
==225604==    still reachable: 7,574,389 bytes in 71,029 blocks
==225604==                       of which reachable via heuristic:
==225604==                         length64           : 1,020,624 bytes in 3 blocks
==225604==         suppressed: 0 bytes in 0 blocks
==225604== Rerun with --leak-check=full to see details of leaked memory
==225604== 
==225604== For lists of detected and suppressed errors, rerun with: -s
==225604== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)