Error running GenericMonteCarlo mover within MultipleOutputWrapper mover

[Anonymous]

Hello Rosetta Users,

I have been trying to write and test some design protocols using rosetta_scripts. While testing a script, I have come across the following error:

protocols.rosetta_scripts.ParsedProtocol: added mover "net_charge_pep" with filter "true_filter"

protocols.rosetta_scripts.ParsedProtocol: added mover "set_up_foldtree" with filter "true_filter"

protocols.rosetta_scripts.ParsedProtocol: added mover "loop_GMC" with filter "true_filter"

protocols.rosetta_scripts.ParsedProtocol: added mover "clear_netch" with filter "true_filter"

protocols.rosetta_scripts.ParsedProtocol: added mover "collect_design" with filter "true_filter"

protocols.rosetta_scripts.ParsedProtocol: added mover "pose_filter" with filter "true_filter"

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job

protocols.jd2.PDBJobInputter: filling pose from saved copy Top_ectd_0016_hsep3EP1__final_0059.2_0001.pdb

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AddNetChargeConstraintMover - net_charge_pep=======================

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AtomTree - set_up_foldtree=======================

protocols.protein_interface_design.movers.SetAtomTree: Applying fold_tree: FOLD_TREE  EDGE 134 1 -1  EDGE 134 180 -1  EDGE 134 192 1  EDGE 192 181 -1  EDGE 192 202 -1

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER MultipleOutputWrapper - loop_GMC=======================

protocols.simple_moves.GenericMonteCarloMover: [ ERROR ] mover not found in map:

<GenericMonteCarlo drift="1" mover_name="design1_parse" name="peploop_des_protocol" preapply="false" recover_low="1" sample_type="low" scorefxn_name="ref2015_netch_cons" temperature="0.8" trials="1000"/>





ERROR: Assertion `find_mover != movers.end()` failed.

ERROR:: Exit from: src/protocols/simple_moves/GenericMonteCarloMover.cc line: 976

BACKTRACE:

/home/bp-lab/install-fold/rosetta_bin_linux_2018.09.60072_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<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x2ea) [0x7fe1e64398ea]

/home/bp-lab/install-fold/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols.3.so(protocols::simple_moves::GenericMonteCarloMover::parse_my_tag(std::shared_ptr<utility::tag::Tag const>, basic::datacache::DataMap&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::shared_ptr<protocols::filters::Filter>, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<protocols::filters::Filter> > > > const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<protocols::moves::Mover>, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const>, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<protocols::moves::Mover> > > > const&, core::pose::Pose const&)+0x3343) [0x7fe1e35c2be3]

/home/bp-lab/install-fold/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::moves::MoverFactory::newMover(std::shared_ptr<utility::tag::Tag const>, basic::datacache::DataMap&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::shared_ptr<protocols::filters::Filter>, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<protocols::filters::Filter> > > > const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<protocols::moves::Mover>, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const>, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<protocols::moves::Mover> > > > const&, core::pose::Pose const&) const+0x8b) [0x7fe1e722d7db]

/home/bp-lab/install-fold/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::rosetta_scripts::MultipleOutputWrapper::generate_pose(core::pose::Pose&)+0x1c42) [0x7fe1e7621322]

/home/bp-lab/install-fold/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x2ec) [0x7fe1e7648ebc]

/home/bp-lab/install-fold/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair, std::allocator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair> > >)+0x3b) [0x7fe1e764a34b]

/home/bp-lab/install-fold/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1b0) [0x7fe1e764ac00]

/home/bp-lab/install-fold/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/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)+0xbed) [0x7fe1e773f9ad]

/home/bp-lab/install-fold/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x166) [0x7fe1e7741db6]

/home/bp-lab/install-fold/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x57) [0x7fe1e7727d57]

rosetta_scripts.default.linuxgccrelease() [0x402159]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7fe1e5873830]

rosetta_scripts.default.linuxgccrelease() [0x402449]

protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:



File: src/protocols/simple_moves/GenericMonteCarloMover.cc:976

[ ERROR ] UtilityExitException

ERROR: Assertion `find_mover != movers.end()` failed.





protocols.jd2.JobDistributor: [ ERROR ]



[ERROR] Exception caught by JobDistributor for job SA_Top_ectd_0016_hsep3EP1__final_0059.2_0001_0001



File: src/protocols/simple_moves/GenericMonteCarloMover.cc:976

[ ERROR ] UtilityExitException

ERROR: Assertion `find_mover != movers.end()` failed.





protocols.jd2.JobDistributor: [ ERROR ]

protocols.jd2.JobDistributor: [ WARNING ] SA_Top_ectd_0016_hsep3EP1__final_0059.2_0001_0001 reported failure and will NOT retry

protocols.jd2.JobDistributor: no more batches to process...

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 7 seconds

protocols.jd2.JobDistributor: [ WARNING ] The following options have been set, but have not yet been used:

-holes:dalphaball



protocols.toolbox.task_operations.RestrictIdentitiesOperation: Preventing from repacking residues of type(s): PRO Restricting to repacking residues of type(s): PRO

protocols.toolbox.task_operations.RestrictIdentitiesOperation: [ WARNING ] Message(s) above was printed in the end instead of proper place because this Tracer object has some contents left in inner buffer when destructor was called. Explicitly call Tracer::flush() or end your IO with std::endl to disable this warning.

Looking at this, it seems that the GMC mover needs to be defined outside the MultipleOutputWrapper tag, as the erros says “mover not found in map”. However, the documentation doesn’t point towards any such requirement.  There are other warnings too. I am using rosetta version 2018.09. Maybe I have made a minor mistake or some changes have happened, not reflected in the documentation; i am not sure.  Please suggest a solution to this. The xml file is attached herein.

[Anonymous]

Hello again.

I have rectified the problem. The solution was to execute the mover using the full ROSETTASCRIPTS tag within the MultipleOutputWrapper.  Just including the mover tag within the MOM mover does not work. The online documentation on MOM mover seems outdated which is understandable considering that changes in Rosetta occur on a weekly basis.

Lesson learnt: If in doubt, follow the updated documentation the comes  packaged with the rosetta release you install.

Cheers.

 

[Author]

Posts