Using Rosetta source dir at: /home/madhu/Downloads/rosetta_bin_linux_2015.31.58019_bundle/main/source Using Rosetta database dir at: /home/madhu/Downloads/rosetta_bin_linux_2015.31.58019_bundle/main/database No command file found for zinc_homodimer_design. Skipping. No command file found for zinc_heterodimer. Skipping. No command file found for validate_database. Skipping. No command file found for unfolded_state_energy_calc. Skipping. No command file found for torsion_restricted_sampling. Skipping. No command file found for test_idealize. Skipping. No command file found for symmetric_docking. Skipping. No command file found for swm_rna_singleloop. Skipping. No command file found for swm_rna_move_two_strands. Skipping. No command file found for swm_rna_move_inside_helix_by_jump. Skipping. No command file found for swm_rna_move_align_dock. Skipping. No command file found for swm_rna_fourwayjunction. Skipping. No command file found for swm_protein_preminimize. Skipping. No command file found for swm_protein_move_inside_coiledcoil_by_bond. Skipping. No command file found for swm_protein_from_scratch. Skipping. No command file found for swa_rna_loop_sampler. Skipping. No command file found for swa_rna_loop_clusterer. Skipping. No command file found for swa_rna_gagu_23_append_and_kic_close. Skipping. No command file found for swa_rna_gagu_22_prepend_and_kic_close. Skipping. No command file found for swa_rna_gagu_20_append_floating_base_by_jump. Skipping. No command file found for swa_rna_gagu_19_prepend_floating_base_by_jump. Skipping. No command file found for swa_rna_gagu_18_rebuild_bulge. Skipping. No command file found for swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide. Skipping. No command file found for swa_rna_gagu_12_helix_addition. Skipping. No command file found for swa_rna_gagu_11_append_and_ccd_close. Skipping. No command file found for swa_rna_gagu_10_prepend_and_ccd_close. Skipping. No command file found for swa_rna_gagu_09_sample_virtual_ribose. Skipping. No command file found for swa_rna_gagu_08_append_dinucleotide. Skipping. No command file found for swa_rna_gagu_07_prepend_dinucleotide. Skipping. No command file found for swa_rna_gagu_06_append_to_3primeterminus. Skipping. No command file found for swa_rna_gagu_05_prepend_to_5primeterminus. Skipping. No command file found for swa_rna_gagu_04_clustering. Skipping. No command file found for swa_rna_gagu_03_append_to_silent. Skipping. No command file found for swa_rna_gagu_02_prepend. Skipping. No command file found for swa_protein_prepack. Skipping. No command file found for swa_protein_loop_sampler. Skipping. No command file found for swa_protein_combine_loops. Skipping. No command file found for swa_protein_cluster. Skipping. No command file found for swa_protein_build_at_Cterminus. Skipping. No command file found for swa_protein_CCDclose. Skipping. No command file found for supercharge. Skipping. No command file found for super_aln. Skipping. No command file found for splice_out_L3_shorter. Skipping. No command file found for splice_out_L3_same. Skipping. No command file found for splice_out_L3_longer. Skipping. No command file found for splice_out_L1_L2_same. Skipping. No command file found for splice_out_H3_same. Skipping. No command file found for splice_out_H3_longer. Skipping. No command file found for splice_out_H1_H2_shorter. Skipping. No command file found for splice_out_H1_H2_longer. Skipping. No command file found for splice_in_4loops_shorter. Skipping. No command file found for sequence_tolerance. Skipping. No command file found for sequence_recovery. Skipping. No command file found for sdf_reader. Skipping. No command file found for score_only_silence. Skipping. No command file found for score_aln. Skipping. No command file found for score12_docking. Skipping. No command file found for rs_loophash. Skipping. No command file found for rs_flexbbmoves. Skipping. No command file found for rotamer_recovery_compare_two_structures. Skipping. No command file found for rotamer_recovery. Skipping. No command file found for rotamer_probability. Skipping. No command file found for rosetta_scripts_hbond_options. Skipping. No command file found for rna_suitename. Skipping. No command file found for rna_minimize. Skipping. No command file found for rna_helix. Skipping. No command file found for rna_design. Skipping. No command file found for rna_denovo. Skipping. No command file found for resource_database_locator. Skipping. No command file found for residue_energy_breakdown. Skipping. No command file found for residue_data_resource. Skipping. No command file found for repack_with_elec_dens. Skipping. No command file found for remodel_helical_repeat. Skipping. No command file found for remodel_disulfides_rosettascripts. Skipping. No command file found for remodel_disulfides. Skipping. No command file found for remodel. Skipping. No command file found for relax_w_allatom_cst. Skipping. No command file found for referencepose_mutateresidue. Skipping. No command file found for readin_dna_rna_protein. Skipping. No command file found for ppk. Skipping. No command file found for posttranslationalmod_io. Skipping. No command file found for pocket_suggest_targets. Skipping. No command file found for pocket_measure. Skipping. No command file found for pmut_scan. Skipping. No command file found for place_simultaneously. Skipping. No command file found for phosphonate. Skipping. No command file found for perturb_helical_bundle_copying_pitch. Skipping. No command file found for per_residue_energies. Skipping. No command file found for pepspec_anchor_dock. Skipping. No command file found for pepspec. Skipping. No command file found for orbitals. Skipping. No command file found for nucleobase_sample_around. Skipping. No command file found for nonideal_rtmin. Skipping. No command file found for next_generation_KIC. Skipping. No command file found for ncaa_fixbb. Skipping. No command file found for mr_protocols. Skipping. No command file found for mpi_multistate_design. Skipping. No command file found for mp_symmetry_load. Skipping. No command file found for mp_relax_w_ligand. Skipping. No command file found for mp_relax. Skipping. No command file found for mp_dock_prepack. Skipping. No command file found for motif_extraction. Skipping. No command file found for molfile_to_params. Skipping. No command file found for minimize_with_elec_dens. Skipping. No command file found for mg_modeler_lores. Skipping. No command file found for mg_modeler. Skipping. No command file found for metalloprotein_abrelax. Skipping. No command file found for membrane_relax. Skipping. No command file found for match_6cpa. Skipping. No command file found for match_1n9l. Skipping. No command file found for match_1c2t. Skipping. No command file found for make_symmdef_file. Skipping. No command file found for make_rot_lib. Skipping. No command file found for make_exemplar. Skipping. No command file found for make_and_perturb_bundle_multirepeat. Skipping. No command file found for loop_modeling. Skipping. No command file found for ligand_water_docking. Skipping. No command file found for ligand_motif_design. Skipping. No command file found for ligand_dock_script. Skipping. No command file found for ligand_dock_grid. Skipping. No command file found for ligand_dock_7cpa. Skipping. No command file found for kinematic_looprelax. Skipping. No command file found for hybridization. Skipping. No command file found for hts_io. Skipping. No command file found for hotspot_graft. Skipping. No command file found for helical_bundle. Skipping. No command file found for grid_scores_features. Skipping. No command file found for geometric_solvation. Skipping. No command file found for genkic_bin_sampling. Skipping. No command file found for genkic_bin_perturbing. Skipping. No command file found for gen_lig_grids. Skipping. No command file found for gen_apo_grids. Skipping. No command file found for fuzzy. Skipping. No command file found for fragment_picker. Skipping. No command file found for fold_and_dock. Skipping. No command file found for flexpepdock_abinitio. Skipping. No command file found for flexpepdock. Skipping. No command file found for fixbb_resource_manager. Skipping. No command file found for fixbb. Skipping. No command file found for fix_alignment_to_match_pdb. Skipping. No command file found for file_list_locator. Skipping. No command file found for fiber_diffraction_fad. Skipping. No command file found for features_scientific_benchmark. Skipping. No command file found for features_postgres. Skipping. No command file found for features_pdb. Skipping. No command file found for features_parallel. Skipping. No command file found for favor_native_residue. Skipping. No command file found for fast_relax. Skipping. No command file found for extract_pdbs. Skipping. No command file found for extract_atomtree_diffs. Skipping. No command file found for erraser_minimize. Skipping. No command file found for entropy_correction. Skipping. No command file found for doug_dock_design_min_mod2_cal_cal. Skipping. No command file found for docking_low_res. Skipping. No command file found for docking_local_refine_min. Skipping. No command file found for docking_local_refine. Skipping. No command file found for docking_full_protocol. Skipping. No command file found for docking_ensemble. Skipping. No command file found for docking_distance_constraints. Skipping. No command file found for dock_with_hotspot_place_simultaneously. Skipping. No command file found for dna_interface_design. Skipping. No command file found for density_refine_symm. Skipping. No command file found for density_refine. Skipping. No command file found for ddG_scan. Skipping. No command file found for ddG_of_mutation. Skipping. No command file found for ddG_ensemble. Skipping. No command file found for cstfile_to_theozyme_pdb. Skipping. No command file found for cs_rosetta_rna. Skipping. No command file found for coupled_moves. Skipping. No command file found for contactMap. Skipping. No command file found for combine_silent. Skipping. No command file found for code_duplication. Skipping. No command file found for cluster_filter. Skipping. No command file found for cluster_alns. Skipping. No command file found for cluster. Skipping. No command file found for classic_relax_1a19. Skipping. No command file found for centroid_disulfide_scores. Skipping. No command file found for bundlereporter_filter. Skipping. No command file found for bundlegridsampler_z0_offset. Skipping. No command file found for bundlegridsampler_copy_pitch. Skipping. No command file found for bundlegridsampler_composition_energy. Skipping. No command file found for bundlegridsampler. Skipping. No command file found for bin_perturbation. Skipping. No command file found for bin_initialization. Skipping. No command file found for backbonegridsampler_multiresidue. Skipping. No command file found for backbonegridsampler. Skipping. No command file found for app_exception_handling. Skipping. No command file found for antibody_graft. Skipping. No command file found for antibody_H3. Skipping. No command file found for add_job_pair_data. Skipping. No command file found for abinitio. Skipping. No command file found for UBQ_Gp_LYX-Cterm. Skipping. No command file found for UBQ_Gp_CYD-CYD. Skipping. No command file found for UBQ_E2_thioester_two_ubiquitins. Skipping. No command file found for UBQ_E2_thioester_extra_bodies. Skipping. No command file found for UBQ_E2_thioester. Skipping. No command file found for ProQ. Skipping. No command file found for LayerDesign_ncaas. Skipping. No command file found for LayerDesign. Skipping. No command file found for InterfaceAnalyzer_tracer. Skipping. No command file found for InterfaceAnalyzer_prepack. Skipping. No command file found for InterfaceAnalyzer_bothpack. Skipping. No command file found for InterfaceAnalyzer. Skipping. No command file found for HOW_TO_MAKE_TESTS. Skipping. No command file found for FloppyTail. Skipping. No command file found for Enzrevert_xml. Skipping. No command file found for DARC_shapeonly. Skipping. No command file found for DARC_electrostatics. Skipping. No command file found for BuildPeptide. Skipping. No command file found for AnchoredPDBCreator. Skipping. No command file found for AlterSpecDisruption. Skipping. Running Test bundlegridsampler_design_nstruct_mode bash /home/madhu/Downloads/rosetta_bin_linux_2015.31.58019_bundle/main/tests/integration/new/bundlegridsampler_design_nstruct_mode/command.mpi.sh Encounter error while executing: bash /home/madhu/Downloads/rosetta_bin_linux_2015.31.58019_bundle/main/tests/integration/new/bundlegridsampler_design_nstruct_mode/command.mpi.sh *** Test bundlegridsampler_design_nstruct_mode did not run! Check your --mode flag and paths. [2016-05-09 14:13:01.977752] Finished bundlegridsampler_design_nstruct_mode in 1 seconds [~ 212 test (73%) started, 75 in queue, 211 running] No command file found for zinc_homodimer_setup. Skipping. No command file found for write_mol_file. Skipping. No command file found for vip. Skipping. No command file found for symmetry_data_resource. Skipping. No command file found for swm_rna_nickedhelix. Skipping. No command file found for swm_rna_move_inside_helix_by_bond. Skipping. No command file found for swm_rna_loop_design. Skipping. No command file found for swm_protein_move_inside_helix_by_bond. Skipping. No command file found for swm_protein_loop_sampler. Skipping. No command file found for swm_protein_CCDmove. Skipping. No command file found for swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump. Skipping. No command file found for swa_rna_gagu_17_append_floating_base. Skipping. No command file found for swa_rna_gagu_15_combine_long_loop_sampling. Skipping. No command file found for swa_rna_gagu_14_combine_long_loop_filtering. Skipping. No command file found for swa_rna_gagu_13_chunk_combination_and_closure. Skipping. No command file found for swa_rna_gagu_01_append. Skipping. No command file found for swa_rna_erraser. Skipping. No command file found for swa_protein_build_at_Nterminus. Skipping. No command file found for surface_docking. Skipping. No command file found for splice_out_generic. Skipping. No command file found for splice_out_L1_L2_shorter. Skipping. No command file found for splice_out_L1_L2_longer. Skipping. No command file found for splice_out_H3_shorter. Skipping. No command file found for splice_out_H1_H2_same. Skipping. No command file found for splice_in_4loops_same_length. Skipping. No command file found for splice_in_4loops_longer. Skipping. No command file found for set_torsion. Skipping. No command file found for select_best_unique_ligand_poses. Skipping. No command file found for rosetta_scripts_setup. Skipping. No command file found for rosetta_scripts_loops. Skipping. No command file found for rna_score. Skipping. No command file found for rna_cluster. Skipping. No command file found for rna_assemble. Skipping. No command file found for resource_database_tables. Skipping. No command file found for recces_turner. Skipping. No command file found for pocket_relax. Skipping. No command file found for perturb_helical_bundle_z_offset. Skipping. No command file found for perturb_helical_bundle. Skipping. No command file found for oop_design. Skipping. No command file found for noe_assignment. Skipping. No command file found for msd_mover. Skipping. No command file found for mp_symdock. Skipping. No command file found for mp_score_jd2. Skipping. No command file found for mp_dock. Skipping. No command file found for motif_score_filter. Skipping. No command file found for membrane_relax_hbond. Skipping. No command file found for membrane_abinitio. Skipping. No command file found for kinemage_grid_output. Skipping. No command file found for helical_bundle_nonideal. Skipping. No command file found for hbs_design. Skipping. No command file found for genkic_bin_setting. Skipping. No command file found for fold_cst_new. Skipping. No command file found for features. Skipping. No command file found for enzdes. Skipping. No command file found for docking_site_constraints. Skipping. No command file found for docking_prepack. Skipping. No command file found for docking_ensemble_prepack. Skipping. No command file found for database_session_resource. Skipping. No command file found for bundlegridsampler_z1_offset. Skipping. No command file found for bundlegridsampler_multirepeat. Skipping. No command file found for bundlegridsampler_design. Skipping. No command file found for beta_strand_homodimer. Skipping. No command file found for backrub. Skipping. No command file found for Werror_check. Skipping. No command file found for RBOut. Skipping. No command file found for KIC_with_fragments. Skipping. No command file found for KIC_vicinity. Skipping. No command file found for KIC_refine. Skipping. No command file found for InterfaceAnalyzer_resfile. Skipping. No command file found for InterfaceAnalyzer_allscores. Skipping. No command file found for DARC_sampling_on_the_fly. Skipping. No command file found for DARC_make_ray_files. Skipping. No command file found for AnchoredDesign. Skipping. No command file found for AnchorFinder. Skipping. Running Test backbonegridsampler_nstruct_mode bash /home/madhu/Downloads/rosetta_bin_linux_2015.31.58019_bundle/main/tests/integration/new/backbonegridsampler_nstruct_mode/command.mpi.sh grep: log_1: No such file or directory rm: cannot remove ‘log_1’: No such file or directory grep: log_2: No such file or directory rm: cannot remove ‘log_2’: No such file or directory grep: log_3: No such file or directory rm: cannot remove ‘log_3’: No such file or directory Finished backbonegridsampler_nstruct_mode in 8 seconds [~ 287 test (100%) started, 0 in queue, 285 running] FAIL bundlegridsampler_design_nstruct_mode nonempty diff ref/bundlegridsampler_design_nstruct_mode/.test_did_not_run.log new/bundlegridsampler_design_nstruct_mode/.test_did_not_run.log FAIL backbonegridsampler_nstruct_mode nonempty diff ref/backbonegridsampler_nstruct_mode/score_sorted.sc new/backbonegridsampler_nstruct_mode/score_sorted.sc