pdb = model_real_space_refined.pdb map = ../maps/FFT_13/70S_converted_1.ccp4 out_pdb = map_reso = 3.73 rna_prot_erraser = False debug = False rosetta_folder = rosetta_bin = rosetta_database = nproc = 0 multiproc_minimize = False guarantee_no_DNA = False n_iterate = 1 rebuild_rmsd = True rebuild_all = False ['/home/mbelouso/rosetta3.7/tools/ERRASER/erraser.py', '-pdb', 'model_real_space_refined.pdb', '-map', '../maps/FFT_13/70S_converted_1.ccp4', '-map_reso', '3.73'] fixed_res = [] ['/home/mbelouso/rosetta3.7/tools/ERRASER/erraser.py', '-pdb', 'model_real_space_refined.pdb', '-map', '../maps/FFT_13/70S_converted_1.ccp4', '-map_reso', '3.73'] rebuild_extra_res = [] use_native_edensity_cutoff = False constrain_chi = True native_screen_RMSD = 3.0 search_syn_pyrimidine_only_when_native_syn = True num_pose_kept = 100 num_pose_kept_cluster = 10 o2prime_legacy_mode = True scoring_file = use_2prime_OH_potential = False fcc2012_new_torsional_potential = True fcc2012_scoring_file = True enlarge_H_lj = True ################################### Starting erraser... Temporary directory /home/mbelouso/l1/EM/VRE/LinR2_Faecalis/70S/erraser01/model_real_space_refined_erraser_temp/ exists... Use the data stored in the existing folder. Because -use_existing_temp_folder is set to True. ######Start submitting the Rosetta command for rna_rosetta_ready_set######## core.init: Rosetta version from core.init: command: /home/mbelouso/rosetta3.7/main/source/bin/erraser_minimizer.linuxgccrelease -database /home/mbelouso/rosetta3.7/main/database/ -s start.pdb -ready_set_only true -ignore_unrecognized_res -inout:skip_connect_info true -in:guarantee_no_DNA false -output_virtual true core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1272810019 seed_offset=0 real_seed=-1272810019 core.init.random: RandomGenerator:init: Normal mode, seed=-1272810019 RG_type=mt19937 protocols.jd2.JobInputterFactory: Available : ERROR: PDBJobInputter is not known to the JobInputterFactory. Was it registered via a JobInputterRegistrator in one of the init.cc files (devel/init.cc or protocols/init.cc)? ERROR:: Exit from: src/protocols/jd2/JobInputterFactory.cc line: 97 /home/mbelouso/rosetta3.7/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/python/libutility.so(print_backtrace(char const*)+0x3e) [0x7f3664e5b21e] /home/mbelouso/rosetta3.7/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/python/libutility.so(utility::exit(std::__cxx11::basic_string, std::allocator > const&, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x19e) [0x7f3664e5b07e] /home/mbelouso/rosetta3.7/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/python/libprotocols.1.so(protocols::jd2::JobInputterFactory::get_JobInputter_from_string(std::__cxx11::basic_string, std::allocator > const&)+0x22e) [0x7f3667eec1ce] /home/mbelouso/rosetta3.7/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/python/libprotocols.1.so(protocols::jd2::JobInputterFactory::get_new_JobInputter()+0x10bf) [0x7f3667eee2cf] /home/mbelouso/rosetta3.7/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/python/libprotocols.1.so(protocols::jd2::JobDistributorFactory::create_job_inputter()+0x31) [0x7f3667ee9ef1] /home/mbelouso/rosetta3.7/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/python/libprotocols.1.so(protocols::jd2::JobDistributor::init_jd()+0x273) [0x7f3667ee2703] /home/mbelouso/rosetta3.7/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/python/libprotocols.1.so(protocols::jd2::JobDistributor::JobDistributor()+0xd3) [0x7f3667ee7e53] /home/mbelouso/rosetta3.7/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/python/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::FileSystemJobDistributor()+0x3a) [0x7f3667eb3fda] /home/mbelouso/rosetta3.7/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/python/libprotocols.1.so(protocols::jd2::JobDistributorFactory::create_job_distributor()+0x4ee) [0x7f3667eea95e] /home/mbelouso/rosetta3.7/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/python/libprotocols.1.so(protocols::jd2::JobDistributor::get_instance()+0x116) [0x7f3667ee85a6] /home/mbelouso/rosetta3.7/main/source/bin/erraser_minimizer.linuxgccrelease() [0x404db4] /home/mbelouso/rosetta3.7/main/source/bin/erraser_minimizer.linuxgccrelease() [0x4037d1] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f3664209830] /home/mbelouso/rosetta3.7/main/source/bin/erraser_minimizer.linuxgccrelease() [0x404c69] Traceback (most recent call last): File "/home/mbelouso/rosetta3.7/tools/ERRASER/erraser.py", line 16, in erraser( option ) File "/home/mbelouso/rosetta3.7/tools/ERRASER/erraser_wrapper.py", line 54, in erraser rna_rosetta_ready_set('start.pdb', 'minimize_0.pdb', option, option.rosetta_bin, option.rosetta_database, option.rna_prot_erraser) File "/home/mbelouso/rosetta3.7/tools/ERRASER/erraser_util.py", line 363, in rna_rosetta_ready_set subprocess_call( command, sys.stdout, sys.stderr ) File "/home/mbelouso/rosetta3.7/tools/ERRASER/erraser_util.py", line 101, in subprocess_call subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel) File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/home/mbelouso/rosetta3.7/main/source/bin/erraser_minimizer.linuxgccrelease -database /home/mbelouso/rosetta3.7/main/database/ -s start.pdb -ready_set_only true -ignore_unrecognized_res -inout:skip_connect_info true -in:guarantee_no_DNA false -output_virtual true' returned non-zero exit status -11