You are here

Job Distribution Error

3 posts / 0 new
Last post
Job Distribution Error
#1

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(2,8) 
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?

 

Category: 
Post Situation: 
Mon, 2020-02-10 08:22
ac.research

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".

Thu, 2020-02-13 15:26
vmulligan

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?

Fri, 2020-02-14 23:33
ac.research