Job Distribution Error – Rosetta Commons

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February 10, 2020 at 4:22 pm #3342

Anonymous

Hello,

I am having a similar issue with the job destribution for the script from the koga 2012 paper:

Script:



<ROSETTASCRIPTS>

<SCOREFXNS>

<ScoreFunction name="SFXN1" weights="fldsgn_cen" >

<Reweight scoretype="hbond_sr_bb" weight="1.0" />

<Reweight scoretype="hbond_lr_bb" weight="1.0" />

</ScoreFunction>

<ScoreFunction name="SFXN2" weights="fldsgn_cen" >

<Reweight scoretype="hbond_sr_bb" weight="1.0" />

<Reweight scoretype="hbond_lr_bb" weight="1.0" />

</ScoreFunction>

<ScoreFunction name="SFXN3" weights="myweight" >

<Reweight scoretype="atom_pair_constraint" weight="1.0" />

</ScoreFunction>

</SCOREFXNS>

<FILTERS>

<SheetTopology name="st1" topology="1-3.A.0;2-3.A.0" blueprint="./input1.bbskel" />

<HelixKink name="hk1" blueprint="./input1.bbskel" />

<CompoundStatement name="cm1" >

<AND filter_name="st1"/>

<AND filter_name="hk1"/>

</CompoundStatement>

<SheetTopology name="st2" topology="1-3.A.0;1-4.A.0;2-3.A.0" blueprint="./input2.bbskel" />

<HelixKink name="hk2" blueprint="./input2.bbskel" />

<HelixPairing name="hp" helix_pairings="1-2.A" dist="13.0" cross="30.0" align="5.0" blueprint="./input2.bbskel" />

<CompoundStatement name="cm2" >

<AND filter_name="st2"/>

<AND filter_name="hk2"/>

<AND filter_name="hp"/>

</CompoundStatement>

<SecondaryStructure name="ss" blueprint="./input2.bbskel" />

<ScoreType name="sc" scorefxn="talaris2014" score_type="total_score" threshold="-170"/>

<PackStat name="pstat" threshold="0.6" />

</FILTERS>

<TASKOPERATIONS>

<LimitAromaChi2 name="limitchi2" />

<LayerDesign name="layer_all" layer="core_boundary_surface"  core_H="15" core_E="15" core_L="25" surface_H="60" surface_E="60" surface_L="40" pore_radius="2.0" verbose="true" />

</TASKOPERATIONS>

<MOVERS>

<SetSecStructEnergies name="sse1" scorefxn="SFXN1" blueprint="./input1.bbskel" />

<BluePrintBDR name="bdr1" scorefxn="SFXN1" use_abego_bias="1" blueprint="./input1.bbskel" />

<LoopOver name="lover1" mover_name="bdr1" filter_name="cm1" iterations="10" drift="0" ms_whenfail="FAIL_DO_NOT_RETRY"/>

<SetSecStructEnergies name="sse2" scorefxn="SFXN2" blueprint="./input2.bbskel" />

<BluePrintBDR name="bdr2" scorefxn="SFXN2" use_abego_bias="1" blueprint="./input2.bbskel" />

<LoopOver name="lover2" mover_name="bdr2" filter_name="cm2" iterations="10" drift="0" ms_whenfail="FAIL_DO_NOT_RETRY"/>

<FlxbbDesign name="flxbb1" ncycles="1" constraints_sheet="10.0" sfxn_design="SFXN3" sfxn_relax="SFXN3" clear_all_residues="1" task_operations="limitchi2,layer_all" blueprint="./input2.bbskel" resfile="./input.resfile" />

<Dssp name="dssp"/>

<FlxbbDesign name="flxbb2" ncycles="1" constraints_sheet="10.0" sfxn_design="SFXN3" sfxn_relax="SFXN3" clear_all_residues="1" task_operations="limitchi2,layer_all" blueprint="./input2.bbskel" resfile="./input.resfile" />

</MOVERS>

<APPLY_TO_POSE>

</APPLY_TO_POSE>

<PROTOCOLS>

<Add mover_name="sse1"/>

<Add mover_name="lover1"/>

<Add mover_name="sse2"/>

<Add mover_name="lover2"/>

<Add mover_name="flxbb1"/>



Add mover_name="dssp"/>

Add filter_name="ss"/>

Add filter_name="hp"/>

Add filter_name="sc"/>

Add mover_name="flxbb2"/>

Add mover_name="dssp"/>

Add filter_name="ss"/>

Add filter_name="pstat"/>

Add filter_name="sc"/>

</PROTOCOLS>

</ROSETTASCRIPTS>

Error:



protocols.forge.remodel.RemodelMover:

protocols.moves.MonteCarlo: MC: 2  -4.81738  -33.2563  -4.81738  -33.2563  0  0  0  rejected

protocols.moves.TrialCounter:             frag trials=  11520;  accepts= 0.4908;  energy_drop/trial=   0.00103

protocols.forge.remodel.RemodelMover:      start stop cut cbreak

protocols.forge.remodel.RemodelMover:      1 48 0 0

protocols.forge.remodel.RemodelMover: ** boost_closure_stage

protocols.forge.remodel.RemodelMover:    n_loops = 0

protocols.forge.remodel.RemodelMover:    no loops to work on with boost_closure. returning.

protocols.forge.remodel.RemodelMover: * 1 / 1   closed / attempts

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014.wts

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

core.pack.pack_rotamers: built 0 rotamers at 0 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

core.pack.interaction_graph.interaction_graph_factory: IG: 480 bytes

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014.wts

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

core.pack.pack_rotamers: built 0 rotamers at 0 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

core.pack.interaction_graph.interaction_graph_factory: IG: 480 bytes

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014.wts

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

core.pack.pack_rotamers: built 0 rotamers at 0 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

core.pack.interaction_graph.interaction_graph_factory: IG: 480 bytes

protocols.fldsgn.filters.SheetTopologyFilter: Topology 1-3.A.0;2-3.A.0 will be filtered

protocols.fldsgn.filters.SheetTopologyFilter: strands = 1-3

protocols.fldsgn.filters.SheetTopologyFilter: strands = 2-3

protocols.topology.StrandPairing: strand1=1(2,

protocols.topology.StrandPairing: strand2=3(41,47)

protocols.topology.StrandPairing: abego=[E, B, B, B, B, B, B, B, A, A, B, A, A, A, A, A, A, A, A, A, A, A, A, A, A, A, A, A, A, G, B, B, B, B, B, B, B, B, G, G, B, B, B, B, B, B, B, O]

protocols.topology.StrandPairing: Computing bulges between 2 and 8

protocols.topology.StrandPairing: Computing bulges between 41 and 47

protocols.topology.StrandPairing: Bulges1: [] Bulges2: []

protocols.topology.StrandPairing: strand1=2(32,38)

protocols.topology.StrandPairing: strand2=3(41,47)

protocols.topology.StrandPairing: abego=[E, B, B, B, B, B, B, B, A, A, B, A, A, A, A, A, A, A, A, A, A, A, A, A, A, A, A, A, A, G, B, B, B, B, B, B, B, B, G, G, B, B, B, B, B, B, B, O]

protocols.topology.StrandPairing: Computing bulges between 32 and 38

protocols.topology.StrandPairing: Computing bulges between 41 and 47

protocols.topology.StrandPairing: Bulges1: [] Bulges2: []

protocols.fldsgn.filters.SheetTopologyFilter: spairset_filter: 1-3.A.0;2-3.A.0

protocols.fldsgn.filters.SheetTopologyFilter: spairset: 1-3.A.0;2-3.A.0

protocols.fldsgn.filters.SheetTopologyFilter: Computing residue pairings for 1-3.A.0: 2-8.47-41

protocols.fldsgn.filters.SheetTopologyFilter: Computing residue pairings for 2-3.A.0: 32-38.47-41

protocols.fldsgn.filters.SheetTopologyFilter: Computing residue pairings for 1-3.A.0: 2-4.47-45

protocols.fldsgn.filters.SheetTopologyFilter: Computing residue pairings for 2-3.A.0: 32-38.47-41

protocols.fldsgn.filters.SheetTopologyFilter: Filtered residue pairings: (2, 47), (3, 46), (4, 45), (5, 44), (6, 43), (7, 42), (8, 41), ], [(32, 47), (33, 46), (34, 45), (35, 44), (36, 43), (37, 42), (38, 41),

protocols.fldsgn.filters.SheetTopologyFilter: Residue pairings in pose: (2, 47), (3, 46), (4, 45), ], [(32, 47), (33, 46), (34, 45), (35, 44), (36, 43), (37, 42), (38, 41),

protocols.fldsgn.filters.SheetTopologyFilter: SheetTopology: Good / Total sheet residues = 10 / 14

protocols.fldsgn.filters.SheetTopologyFilter: Sheet topology 1-3.A.0;2-3.A.0 is not present. Fraction of pairings present: 0.714286

protocols.filters.Filter: CompoundFilter subfilter st1 failed.

protocols.filters.Filter: CompoundFilter as a whole  failed.

protocols.filters.Filter: Compound logical statement is 0.

protocols.rosetta_scripts.ParsedProtocol: Mover LoopOver reports failure!

protocols.jd2.JobDistributor: [ WARNING ] input_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 163 seconds

Error: [ ERROR ] Exception caught by rosetta_scripts application:



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

1 jobs failed; check output for error messages

Error: [ ERROR ]

The command I used was

/home/acresearch/Rosetta/main/source/bin/rosetta_scripts.linuxgccrelease -s input.pdb -parser:protocol input.xml -nstruct 1 -restortalaris_behavior

Can you help me identify what is causing the error so I can fix it?

February 13, 2020 at 11:26 pm #15146

Anonymous

The output log tells you what happened: one of your filters rejected the structure, so the job distributor is just telling you that that job failed. There was no crash or program error — it’s just a filter that returned “fail”.

February 15, 2020 at 7:33 am #15147

Anonymous

Ah I see,

OK so it seems the SheetTopology and the HelixPairing filters are what is causing these problems. here is the segment with them commented out:



        <FILTERS>

SheetTopology name="st1" topology="1-3.A.0;2-3.A.0" blueprint="./input1.bbskel" /> <

<HelixKink name="hk1" blueprint="./input1.bbskel" />

<CompoundStatement name="cm1" >

AND filter_name="st1"/>     <

<AND filter_name="hk1"/>

</CompoundStatement>

SheetTopology name="st2" topology="1-3.A.0;1-4.A.0;2-3.A.0" blueprint="./input2.bbskel" /> <

<HelixKink name="hk2" blueprint="./input2.bbskel" />

HelixPairing name="hp" helix_pairings="1-2.A" dist="13.0" cross="30.0" align="5.0" blueprint="./input2.bbskel" /> <

<CompoundStatement name="cm2" >

AND filter_name="st2"/> <

<AND filter_name="hk2"/>

AND filter_name="hp"/> <

</CompoundStatement>

<SecondaryStructure name="ss" blueprint="./input2.bbskel" />

<ScoreType name="sc" scorefxn="talaris2014" score_type="total_score" threshold="-170"/>

<PackStat name="pstat" threshold="0.6" />

</FILTERS>

How can I fix them?

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