Program frozen at “protocols.jobdist.JobDistributors: (0) Master Node — Waiting for job request; tag_ = 1”

Hello,

      The Rosetta program was frozen at “protocols.jobdist.JobDistributors: (0) Master Node — Waiting for job request; tag_ = 1” when I was trying to predict structure of a sequence. Dose anybody know how to solve this problem?

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IU-Quota version 1.2 loaded.

xy32@elogin1:~> :~> module unload PrgEnv-intel

:~: command not found

xy32@elogin1:~> module unload PrgEnv-intel

xy32@elogin1:~> module load PrgEnv-gnu

xy32@elogin1:~> module load openmpi/gnu/4.0.2

openmpi version 4.0.2 loaded.

xy32@elogin1:~> module load rosetta

rosetta version 2019.35 loaded.

xy32@elogin1:~> ls

1ELW.fasta  aat000_03_05.200_v1_3  flags   t000_.psipred_ss2

1elw.pdb    aat000_09_05.200_v1_3  

xy32@elogin1:~> /N/soft/cle6/rosetta/gnu/rosetta_src_2019.35.60890_bundle/main/source/bin/AbinitioRelax.mpi.linuxgccrelease @flags

core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags 

core.init: (0) Rosetta version: rosetta.source.release-231 r231 2019.35+release.767c1ea 767c1ea25c572fbc078db45ad65dddb507240ad3 https://www.rosettacommons.org 2019-08-30T10:52:08.483471

core.init: (0) command: /N/soft/cle6/rosetta/gnu/rosetta_src_2019.35.60890_bundle/main/source/bin/AbinitioRelax.mpi.linuxgccrelease @flags

basic.random.init_random_generator: (0) ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-53430990 seed_offset=0 real_seed=-53430990

basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=-53430990 RG_type=mt19937

core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set.  Created 980 residue types

core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 1.03723 seconds.

core.import_pose.import_pose: (0) File ‘./1elw.pdb’ automatically determined to be of type PDB

core.chemical.GlobalResidueTypeSet: (0) Loading (but possibly not actually using) ‘NI’ from the PDB components dictionary for residue type ‘pdb_NI’

core.chemical.GlobalResidueTypeSet: (0) Loading (but possibly not actually using) ‘TRS’ from the PDB components dictionary for residue type ‘pdb_TRS’

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CG  on residue GLU:NtermProteinFull 1

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CD  on residue GLU:NtermProteinFull 1

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE1 on residue GLU:NtermProteinFull 1

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE2 on residue GLU:NtermProteinFull 1

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CG  on residue MET:NtermProteinFull 122

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  SD  on residue MET:NtermProteinFull 122

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CE  on residue MET:NtermProteinFull 122

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CG  on residue GLU 123

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CD  on residue GLU 123

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE1 on residue GLU 123

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE2 on residue GLU 123

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CG  on residue GLU 231

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CD  on residue GLU 231

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE1 on residue GLU 231

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE2 on residue GLU 231

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OXT on residue MET:CtermProteinFull 236

core.pack.pack_missing_sidechains: (0) packing residue number 1 because of missing atom number 6 atom name  CG 

core.pack.pack_missing_sidechains: (0) packing residue number 122 because of missing atom number 6 atom name  CG 

core.pack.pack_missing_sidechains: (0) packing residue number 123 because of missing atom number 6 atom name  CG 

core.pack.pack_missing_sidechains: (0) packing residue number 231 because of missing atom number 6 atom name  CG 

core.pack.task: (0) Packer task: initialize from command line() 

core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015

core.scoring.etable: (0) Starting energy table calculation

core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well

core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)

core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)

core.scoring.etable: (0) Finished calculating energy tables.

basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv

basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv

basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv

basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv

basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv

basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/all.ramaProb

basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb

basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt

basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt

basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt

basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt

basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA

basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n

core.scoring.P_AA: (0) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.

basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop

basic.io.database: (0) Database file opened: scoring/score_functions/elec_cp_reps.dat

core.scoring.elec.util: (0) Read 40 countpair representative atoms

core.pack.dunbrack.RotamerLibrary: (0) shapovalov_lib_fixes_enable option is true.

core.pack.dunbrack.RotamerLibrary: (0) shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.

core.pack.dunbrack.RotamerLibrary: (0) Binary rotamer library selected: /N/soft/cle6/rosetta/gnu/rosetta_src_2019.35.60890_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin

core.pack.dunbrack.RotamerLibrary: (0) Using Dunbrack library binary file ‘/N/soft/cle6/rosetta/gnu/rosetta_src_2019.35.60890_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin’.

core.pack.dunbrack.RotamerLibrary: (0) Dunbrack 2010 library took 0.154166 seconds to load from binary

core.pack.pack_rotamers: (0) built 63 rotamers at 4 positions.

core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph

core.chemical.GlobalResidueTypeSet: (0) Finished initializing centroid residue type set.  Created 62 residue types

core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 0.029976 seconds.

core.chemical.residue_support: (0) [ WARNING ] Atom type ‘Ni’ on atom ‘NI’ from residue type ‘NI’ does not have a centroid mode equivalent: assuming CAbb.

core.chemical.GlobalResidueTypeSet: (0) Loading (but possibly not actually using) ‘NI’ from the PDB components dictionary for residue type ‘pdb_NI’

core.chemical.GlobalResidueTypeSet: (0) Loading (but possibly not actually using) ‘TRS’ from the PDB components dictionary for residue type ‘pdb_TRS’

protocols.abinitio.AbrelaxApplication: (0) read fasta sequence: 120 residues

GCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEARD

core.import_pose.import_pose: (0) File ‘./1elw.pdb’ automatically determined to be of type PDB

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CG  on residue GLU:NtermProteinFull 1

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CD  on residue GLU:NtermProteinFull 1

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE1 on residue GLU:NtermProteinFull 1

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE2 on residue GLU:NtermProteinFull 1

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CG  on residue MET:NtermProteinFull 122

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  SD  on residue MET:NtermProteinFull 122

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CE  on residue MET:NtermProteinFull 122

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CG  on residue GLU 123

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CD  on residue GLU 123

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE1 on residue GLU 123

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE2 on residue GLU 123

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CG  on residue GLU 231

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  CD  on residue GLU 231

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE1 on residue GLU 231

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OE2 on residue GLU 231

core.conformation.Conformation: (0) [ WARNING ] missing heavyatom:  OXT on residue MET:CtermProteinFull 236

core.pack.pack_missing_sidechains: (0) packing residue number 1 because of missing atom number 6 atom name  CG 

core.pack.pack_missing_sidechains: (0) packing residue number 122 because of missing atom number 6 atom name  CG 

core.pack.pack_missing_sidechains: (0) packing residue number 123 because of missing atom number 6 atom name  CG 

core.pack.pack_missing_sidechains: (0) packing residue number 231 because of missing atom number 6 atom name  CG 

core.pack.task: (0) Packer task: initialize from command line() 

core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015

core.pack.pack_rotamers: (0) built 63 rotamers at 4 positions.

core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph

protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active … 

core.io.fragments: (0) reading fragments from file: ./aat000_09_05.200_v1_3 … 

core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader… 

core.fragments.ConstantLengthFragSet: (0) finished reading top 25 9mer fragments from file ./aat000_09_05.200_v1_3

core.io.fragments: (0) reading fragments from file: ./aat000_03_05.200_v1_3 … 

core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader… 

core.fragments.ConstantLengthFragSet: (0) finished reading top 200 3mer fragments from file ./aat000_03_05.200_v1_3

core.fragment: (0) compute strand/loop fractions for 117 residues… 

protocols.abinitio.AbrelaxApplication: (0) run ClassicAbinitio…..

basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt

basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt

basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt

basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt

basic.io.database: (0) Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth

basic.io.database: (0) Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth

core.scoring.ScoreFunction: (0) ATOM_VDW set to CENTROID_ROT_MIN

core.scoring.ramachandran: (0) shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.

basic.io.database: (0) Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb

basic.io.database: (0) Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_params.txt

basic.io.database: (0) Database file opened: scoring/score_functions/centroid_smooth/cen_rot_env_params.txt

basic.io.database: (0) Database file opened: scoring/score_functions/centroid_smooth/cen_rot_cbeta_params.txt

basic.io.database: (0) Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_ang_params.txt

core.scoring.AtomVDW: (0) Openning alternative vdw file: /N/soft/cle6/rosetta/gnu/rosetta_src_2019.35.60890_bundle/main/database/chemical/atom_type_sets/centroid_rot//min.txt

core.scoring.ScoreFunction: (0) ATOM_VDW set to CENTROID_ROT_MIN

core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015

protocols.jobdist.JobDistributors: (0) Node: 0 next_job()

protocols.jobdist.JobDistributors: (0) Master Node — Waiting for job request; tag_ = 1

Killed