ERROR: Specified chain does not exist.

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    • April 5, 2019 at 6:14 pm #3110
      Anonymous

        Hello,

        I am using already preinstalled software Rosetta 3.10 on ComputeCanada (CCDB). I have run demos tutorial of protein-protein docking, was running successfully. Later, I have submitted own protein-protein docking job. I got an error(see below). Please, I need to help solve this problem.

         

        [ajanihar@gra-login3 input_files]$ rosetta_scripts.mpi.linuxiccrelease @docking_full.options -parser:protocol docking_full.xml -out:suffix _full -nstruct 5

        protocols.TaskOperations.RestrictToInterfaceVectorOperation: (0) [ ERROR ] In RestrictToInterfaceVectorOperation: Cannot find interface between chains 1 and 3. Pose only has 2 chains.

        ERROR: Specified chain does not exist.

        ERROR:: Exit from: src/protocols/task_operations/RestrictToInterfaceVectorOperation.cc line: 219

        BACKTRACE:

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x65d) [0x2ba0d45aec8d]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/libprotocols.4.so(protocols::task_operations::RestrictToInterfaceVectorOperation::apply(core::pose::Pose const&, core::pack::task::PackerTask&) const+0xb71) [0x2ba0ca6637f1]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/libcore.4.so(core::pack::task::TaskFactory::modify_task(core::pose::Pose const&, std::shared_ptr<core::pack::task::PackerTask>) const+0x98) [0x2ba0cf22bca8]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/libcore.4.so(core::pack::task::TaskFactory::create_task_and_apply_taskoperations(core::pose::Pose const&) const+0x171) [0x2ba0cf22ba91]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/libprotocols.3.so(protocols::minimization_packing::PackRotamersMover::setup(core::pose::Pose&)+0x4b) [0x2ba0cba1cd2b]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/libprotocols.3.so(protocols::minimization_packing::PackRotamersMover::apply(core::pose::Pose&)+0x36) [0x2ba0cba1c726]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/libprotocols.4.so(protocols::relax::FastRelax::apply(core::pose::Pose&)+0x354b) [0x2ba0ca2cd97b]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x5d2) [0x2ba0cd60e8a2]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/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> > >)+0x32) [0x2ba0cd60f2b2]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x5e3) [0x2ba0cd60bea3]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/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)+0x16cd) [0x2ba0cd73d07d]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x3ce) [0x2ba0cd73a2ae]

        /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.1/rosetta/3.10/bin/../lib/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x55) [0x2ba0cd7323c5]

        rosetta_scripts.mpi.linuxiccrelease() [0x403dec]

        /cvmfs/soft.computecanada.ca/nix/store/63pk88rnmkzjblpxydvrmskkc8ci7cx6-glibc-2.24/lib/libc.so.6(__libc_start_main+0xf0) [0x2ba0d77bc2e0]

        rosetta_scripts.mpi.linuxiccrelease() [0x4024da]

        protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:

        File: src/protocols/task_operations/RestrictToInterfaceVectorOperation.cc:219

        [ ERROR ] UtilityExitException

        ERROR: Specified chain does not exist.

        protocols.jd2.JobDistributor: (0) [ ERROR ]

        [ERROR] Exception caught by JobDistributor for job col_complex_full_0005

        File: src/protocols/task_operations/RestrictToInterfaceVectorOperation.cc:219

        [ ERROR ] UtilityExitException

        ERROR: Specified chain does not exist.

        protocols.jd2.JobDistributor: (0) [ ERROR ]

        protocols.jd2.JobDistributor: (0) [ WARNING ] col_complex_full_0005 reported failure and will NOT retry

        protocols.jd2.JobDistributor: (0) no more batches to process…

        protocols.jd2.JobDistributor: (0) 5 jobs considered, 5 jobs attempted in 40 seconds

        Error: (0) [ ERROR ] Exception caught by rosetta_scripts application:

        File: src/protocols/jd2/JobDistributor.cc:329

        5 jobs failed; check output for error messages

        Error: (0) [ ERROR ]

         

      • April 8, 2019 at 7:16 pm #14648
        Anonymous

          It sounds from the error message (“protocols.TaskOperations.RestrictToInterfaceVectorOperation: (0) [ ERROR ] In RestrictToInterfaceVectorOperation: Cannot find interface between chains 1 and 3. Pose only has 2 chains. “) like the script that you’re running is referring to chains 1 and 3 (or A and C) somewhere, but you have a structure with only two chains (1 and 2 or A and B).   Check the RestrictToInterfaceVector task operation declaration (in the TASK_OPERATIONS section of your input script) and make sure that you’re specifying the correct chains.

          • April 9, 2019 at 1:53 pm #14652
            Anonymous

              Thanks a lot, Vmulligan for your reply.

              Yes, I can see that I have only two chains in a complex.  Input script has given(1,2 and 3,4) that is why the program difficult to run and converted into error. Now, working fine with only 1,2 option.

              Regards,

              Haresh

               

                

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