Task 1624954806

Name	RosettaVS_SAVE_ALL_OUT_NOJRAN_M1_real_specificity_fulldb_IGNORE_THE_REST_ZT9ExJ_9_343_3022839_3_0
Workunit	1445609566
Created	17 Dec 2025, 10:34:11 UTC
Sent	17 Dec 2025, 11:13:24 UTC
Report deadline	20 Dec 2025, 11:13:24 UTC
Received	23 Dec 2025, 10:29:50 UTC
Server state	Over
Outcome	Success
Client state	Done
Exit status	0 (0x00000000)
Computer ID	6332142
Run time	7 hours 21 min 9 sec
CPU time	5 hours 45 min 34 sec
Validate state	Valid
Credit	785.34
Device peak FLOPS	6.00 GFLOPS
Application version	Rosetta Beta v6.06 x86_64-apple-darwin
Peak working set size	1,727.02 MB
Peak swap size	35,559.54 MB
Peak disk usage	25.19 MB
Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
command: rosetta_beta_6.06_x86_64-apple-darwin @M1_real_specificity_fulldb_ZT9ExJ_9_343.flags -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937
Using database: database_f5ae1de8e1/database
Starting watchdog...
Watchdog active.
Starting watchdog...
Watchdog active.
Starting watchdog...
Watchdog active.

[ ERROR ]: Caught exception:


File: src/core/kinematics/Stub.cc:106
Error in Stub::from_four_points(): 

File: src/numeric/xyzVector.hh:654
Cannot create normalized xyzVector from vector of length() zero.  Error occurred when trying to normalize the vector between points A and B.  A=[-52123933457640356129337459605504.000000,-48273554921297129766110585946112.000000,-1999820645721480433514236084224.000000], B=[-52123933457640356129337459605504.000000,-48273554921297129766110585946112.000000,-1999820645721480433514236084224.000000].
 ------------------------ Begin developer's backtrace ------------------------- 
BACKTRACE:
0   rosetta_beta_6.06_x86_64-apple-darw 0x000000010701cec7 backtrace_string(int) + 87
1   rosetta_beta_6.06_x86_64-apple-darw 0x0000000107030a1d utility::excn::Exception::Exception(char const*, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 205
2   rosetta_beta_6.06_x86_64-apple-darw 0x0000000106c0d037 core::kinematics::Stub::from_four_points(numeric::xyzVector<double> const&, numeric::xyzVector<double> const&, numeric::xyzVector<double> const&, numeric::xyzVector<double> const&) + 2071
3   rosetta_beta_6.06_x86_64-apple-darw 0x000000010655c8cf core::scoring::lkball::LKB_ResidueInfo::build_waters(core::conformation::Residue const&, bool) + 895
4   rosetta_beta_6.06_x86_64-apple-darw 0x000000010655c1ae core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo(core::conformation::Residue const&, bool) + 270
5   rosetta_beta_6.06_x86_64-apple-darw 0x0000000103c0eb53 std::__1::shared_ptr<core::scoring::lkball::LKB_ResidueInfo> std::__1::shared_ptr<core::scoring::lkball::LKB_ResidueInfo>::make_shared<core::conformation::Residue const&>(core::conformation::Residue const&) + 83
6   rosetta_beta_6.06_x86_64-apple-darw 0x0000000103bfd7c9 protocols::ligand_docking::ga_ligand_dock::GridScorer::score(core::pose::Pose&, protocols::ligand_docking::ga_ligand_dock::LigandConformer const&, bool) + 777
7   rosetta_beta_6.06_x86_64-apple-darw 0x0000000105411642 core::optimization::ArmijoLineMinimization::Armijo(double, core::optimization::func_1d&) + 130
8   rosetta_beta_6.06_x86_64-apple-darw 0x000000010541135e core::optimization::ArmijoLineMinimization::operator()(utility::vector1<double, std::__1::allocator<double>>&, utility::vector1<double, std::__1::allocator<double>>&) + 494
9   rosetta_beta_6.06_x86_64-apple-darw 0x000000010541a0b9 core::optimization::Minimizer::lbfgs(utility::vector1<double, std::__1::allocator<double>>&, double&, core::optimization::ConvergenceTest&, std::__1::shared_ptr<core::optimization::LineMinimizationAlgorithm>, int, bool) const + 3177
10  rosetta_beta_6.06_x86_64-apple-darw 0x000000010541502f core::optimization::Minimizer::run(utility::vector1<double, std::__1::allocator<double>>&) + 6975
11  rosetta_beta_6.06_x86_64-apple-darw 0x0000000103c0c52c protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(protocols::ligand_docking::ga_ligand_dock::LigandConformer&, core::optimization::MinimizerOptions const&) + 1884
12  rosetta_beta_6.06_x86_64-apple-darw 0x0000000103c09770 protocols::ligand_docking::ga_ligand_dock::GridScorer::optimize(protocols::ligand_docking::ga_ligand_dock::LigandConformer&, utility::vector1<double, std::__1::allocator<double>>, utility::vector1<utility::vector1<protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer, std::__1::allocator<protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer>>, std::__1::allocator<utility::vector1<protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer, std::__1::allocator<protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer>>>>&, protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies&) + 752
13  rosetta_beta_6.06_x86_64-apple-darw 0x0000000103c164b4 protocols::ligand_docking::ga_ligand_dock::GAOptimizer::optimize_generation(utility::vector1<protocols::ligand_docking::ga_ligand_dock::LigandConformer, std::__1::allocator<protocols::ligand_docking::ga_ligand_dock::LigandConformer>>&, utility::vector1<double, std::__1::allocator<double>> const&) + 356
14  rosetta_beta_6.06_x86_64-apple-darw 0x0000000103c0fe52 protocols::ligand_docking::ga_ligand_dock::GAOptimizer::run(utility::vector1<protocols::ligand_docking::ga_ligand_dock::LigandConformer, std::__1::allocator<protocols::ligand_docking::ga_ligand_dock::LigandConformer>>&) + 2850
15  rosetta_beta_6.06_x86_64-apple-darw 0x0000000103c3447b protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(protocols::ligand_docking::ga_ligand_dock::LigandConformer const&, std::__1::shared_ptr<protocols::ligand_docking::ga_ligand_dock::GridScorer>, protocols::ligand_docking::ga_ligand_dock::LigandAligner&, protocols::ligand_docking::ga_ligand_dock::OutputStructureStore&) + 715
16  rosetta_beta_6.06_x86_64-apple-darw 0x0000000103c2a32e protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(core::pose::Pose&) + 14846
17  rosetta_beta_6.06_x86_64-apple-darw 0x000000010521bfd8 protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&) + 1224
18  rosetta_beta_6.06_x86_64-apple-darw 0x000000010521462f protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&) + 1935
19  rosetta_beta_6.06_x86_64-apple-darw 0x000000010510122c protocols::jd2::JobDistributor::run_one_job(std::__1::shared_ptr<protocols::moves::Mover>&, long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&, unsigned long&, unsigned long&, bool) + 8204
20  rosetta_beta_6.06_x86_64-apple-darw 0x00000001050fe572 protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 194
21  rosetta_beta_6.06_x86_64-apple-darw 0x00000001050f9612 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66
22  rosetta_beta_6.06_x86_64-apple-darw 0x00000001050ef0e6 protocols::jd2::BOINCJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 246
23  rosetta_beta_6.06_x86_64-apple-darw 0x000000010263d254 main + 22020
24  dyld                                0x000000020adb7781 start + 3457
 ------------------------- End developer's backtrace -------------------------- 
Starting watchdog...
Watchdog active.
Starting watchdog...
Watchdog active.
Starting watchdog...
Watchdog active.
Starting watchdog...
Watchdog active.
Starting watchdog...
Watchdog active.
======================================================
DONE ::     1 starting structures  20734.8 cpu seconds
This process generated      1 decoys from       1 attempts
======================================================
BOINC :: WS_max 0

BOINC :: Watchdog shutting down...
10:29:11 (1126): called boinc_finish(0)

</stderr_txt>
]]>