Rosetta job distribution error

[Anonymous]

Hi There,

 I am following rosetta protein design but every time I am getting job distribtion error message.  Here is output

 

<ROSETTASCRIPTS>

    <SCOREFXNS>

        <talaris_full weights=talaris2014>

            <Reweight scoretype=”coordinate_constraint” weight=0.4/>

            <Reweight scoretype=”res_type_constraint” weight=0.4/>

        </talaris_full>

        <soft_rep_full weights=soft_rep>

            <Reweight scoretype=”coordinate_constraint” weight=0.4/>

            <Reweight scoretype=”res_type_constraint” weight=0.4/>

        </soft_rep_full>

        <tal_no_pssm weights=talaris2014>

            <Reweight scoretype=”coordinate_constraint” weight=0.4/>

        </tal_no_pssm>

         <talaris_pure weights=talaris2014/>

    </SCOREFXNS>

    <TASKOPERATIONS>

            <InitializeFromCommandline name=init/>

        <RestrictToRepacking name=rtr/>

         <PreventResiduesFromRepacking name=fix_res reference_pdb_id=”input_example.pdb” residues=”1A,2A,3A,4A”/> #any improtant residues

    </TASKOPERATIONS>

    <MOVERS>

            <PackRotamersMover name=soft_repack scorefxn=soft_rep_full task_operations=init,rtr,fix_res/>

            <PackRotamersMover name=hard_repack scorefxn=talaris_full task_operations=init,rtr,fix_res/>

            <RotamerTrialsMinMover name=RTmin scorefxn=talaris_full task_operations=init,rtr,fix_res/>

            <MinMover name=soft_min scorefxn=soft_rep_full chi=1 bb=1 jump=0/>

            <MinMover name=hard_min scorefxn=talaris_full chi=1 bb=1 jump=0/>

            <ConstraintSetMover name=add_CA_cst cst_file=”example.cst”/>

            <ParsedProtocol name = refinement_block> #10 movers

            <Add mover_name=soft_repack/>

            <Add mover_name=soft_min/>

            <Add mover_name=soft_repack/>

            <Add mover_name=hard_min/>

            <Add mover_name=hard_repack/>

            <Add mover_name=hard_min/>

                      <Add mover_name=hard_repack/>

                    <Add mover_name=RTmin/>

                    <Add mover_name=RTmin/>

                    <Add mover_name=hard_min/>

        </ParsedProtocol>

        <LoopOver name = iter4 mover_name = refinement_block iterations = 4/> #16 reacpk+min iterations total

    </MOVERS>

    <FILTERS>

            <ScoreType name=stability_score_full scorefxn=talaris_full score_type=total_score confidence=0 threshold=0/>

            <ScoreType name=stability_without_pssm scorefxn=tal_no_pssm score_type = total_score confidence=0 threshold=0/>

               <ScoreType name=stability_pure scorefxn=talaris_pure score_type=total_score confidence=0 threshold=0/>

        <Rmsd name=rmsd confidence = 0/>

        <Time name=timer/>

    </FILTERS>

    <PROTOCOLS>

    #1st round is soft design and min, 2nd round is soft design hard min, 3rd and 4th round are hard design and min. In the 4th round also include RT min.

            <Add filter_name=timer/>

        <Add mover_name=add_CA_cst/>

            <Add mover_name=iter4/>

            <Add filter_name=stability_score_full/>

            <Add filter_name=stability_without_pssm/>

            <Add filter_name=stability_pure/>

            <Add filter_name=rmsd/>

        <Add filter_name=timer/>

    </PROTOCOLS>

</ROSETTASCRIPTS>

protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts…

protocols.rosetta_scripts.RosettaScriptsParser: …done

protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator…

protocols.rosetta_scripts.RosettaScriptsParser: …done

protocols.rosetta_scripts.RosettaScriptsParser: Validating input script…

Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job ‘input_example_0001’

Error: [ ERROR ]

 

[Anonymous]

Please post the full error here – on first glance, your script needs to have quotes around everything defined with equal signs.  This is a newer change as of a few years ago – to be more in-line with real XML format.  (For all lines) IE – 

 

ScoreType name=stability_score_full scorefxn=talaris_full score_type=total_score confidence=0 threshold=0

 

Should be:

 

ScoreType name=”stability_score_full” scorefxn=”talaris_full” score_type=”total_score” confidence=”0″ threshold=”0″

 

See the docs for more info:

https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/RosettaScripts#example-xml-file

 

[Anonymous]

I have attached  both xml and error file. 

cmd_refine.log is @cmd_refine flag and error message is in log file.

 

command line:

 

$ROSETTA3/bin/rosetta_scripts.linuxgccrelease -database $ROSETTA3_DB -in:file:s input_example.pdb -parser:protocol refine.xml -parser:script_vars res_to_fix=1A,2A,3A,4A -parser:script_vars pdb_reference=input_example.pdb -parser:script_vars cst_full_path=example.cst -parser:script_vars cst_value=0.4 @flags -overwrite

 

 

Thnak you.

 

[Anonymous]

Thanks, yes, The XML will need to be reformatted to have the quotes.  

[Anonymous]

Also, there is a script to do the rewriting.  I didn’t know where it was – but I found it.  It’s in Rosetta/tools xrw_xsd – it’s called rewrite_rosetta_script.py

That will add quotes so you don’t have to do it manually.  Just make sure you downloaded the tools, if not, you can download them from where you downloaded Rosetta.  

[Anonymous]

Thanks  Jadolfbr. Highly appreciate your help and time.

 

[Anonymous]

Hi, all.

I also met Rosetta job distribution error. I really do not know how to solve it. I am wondering anyone could please help me out.

much appreciated !!

<SCOREFXNS>

           <ScoreFunction name=”fa_talaris2014″ weights=”talaris2014″/>

           <ScoreFunction name=”fa_talaris2013_cart” weights=”talaris2013_cart”/>

           <ScoreFunction name=”fa_score12″ weights=”score12″/>

           <ScoreFunction name=”fa_soft_rep” weights=”soft_rep”/>

           <ScoreFunction name=”fa_talaris2013″ weights=”talaris2013″/>

           <ScoreFunction name=”fa_talaris2014_soft_fa_rep” weights=”talaris2014″>

             <Reweight scoretype=”fa_rep” weight=”0.055″/>

 </ScoreFunction>

           <ScoreFunction name=”fa_interface” weights=”interface”/>

        </SCOREFXNS>

        <TASKOPERATIONS>

          <ReadResfile name=”rrf” filename=”../0.1066_data_wuVJqf/3HFM246.mutation.resfile”/>

          <ReadResfile name=”rrf_pack” filename=”../0.1066_data_wuVJqf/3HFM246.pack.resfile”/>

        </TASKOPERATIONS>

 <MOVERS>

          <MinMover name=”minmover” scorefxn=”fa_talaris2014″  chi=”1″ bb=”1″ jump=”ALL” cartesian=”0″ type=”lbfgs_armijo” tolerance=”0.001″/>

          <ddG name=”ddgmover” scorefxn=”fa_score12″ chain_num=”3″ repack_unbound=”false” repack_bound=”false” relax_bound=”false” task_operations=”rrf_pack”/>

        </MOVERS>

        <FILTERS>

          <DdGScan name=”alascan” task_operations=”rrf” repeats=”1″ scorefxn=”fa_score12″ report_diffs=”1″ write2pdb=”1″ ddG_mover=”ddgmover” />

        </FILTERS>

        <MOVERS>

          <ReportToDB name=”3HFM246″ batch_description=”score12″>

            <ResidueFeatures/>

            <PdbDataFeatures/>

            <ScoreTypeFeatures/>

            <ScoreFunctionFeatures scorefxn=”fa_score12″/>

            <StructureScoresFeatures scorefxn=”fa_score12″/>

            <ResidueScoresFeatures scorefxn=”fa_score12″/>

            <DdGFeatures ddG_scan_mover=”alascan”/>

          </ReportToDB>

        </MOVERS>

<APPLY_TO_POSE>

        </APPLY_TO_POSE>

        <PROTOCOLS>

          <Add mover_name=”3HFM246″/>

        </PROTOCOLS>

        <OUTPUT />

</ROSETTASCRIPTS>

protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts…

protocols.rosetta_scripts.RosettaScriptsParser: …done

protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator…

protocols.rosetta_scripts.RosettaScriptsParser: …done

protocols.rosetta_scripts.RosettaScriptsParser: Validating input script…

protocols.rosetta_scripts.RosettaScriptsParser: …done

protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:

<ROSETTASCRIPTS>

 

 <SCOREFXNS>

                <ScoreFunction name=”fa_talaris2014″ weights=”talaris2014″/>

                <ScoreFunction name=”fa_talaris2013_cart” weights=”talaris2013_cart”/>

                <ScoreFunction name=”fa_score12″ weights=”score12″/>

                <ScoreFunction name=”fa_soft_rep” weights=”soft_rep”/>

                <ScoreFunction name=”fa_talaris2013″ weights=”talaris2013″/>

                <ScoreFunction name=”fa_talaris2014_soft_fa_rep” weights=”talaris2014″>

                        <Reweight scoretype=”fa_rep” weight=”0.055″/>

                </ScoreFunction>

                <ScoreFunction name=”fa_talaris2014_soft_fa_dun” weights=”talaris2014″>

                        <Reweight scoretype=”fa_dun” weight=”0.07″/>

                </ScoreFunction>

                <ScoreFunction name=”fa_interface” weights=”interface”/>

        </SCOREFXNS>

        <TASKOPERATIONS>

                <ReadResfile filename=”../0.1066_data_wuVJqf/3HFM246.mutation.resfile” name=”rrf”/>

                <ReadResfile filename=”../0.1066_data_wuVJqf/3HFM246.pack.resfile” name=”rrf_pack”/>

        </TASKOPERATIONS>

        <MOVERS>

                <MinMover bb=”1″ cartesian=”0″ chi=”1″ jump=”ALL” name=”minmover” scorefxn=”fa_talaris2014″ tolerance=”0.001″ type=”lbfgs_armijo”/>

                  <ddG chain_num=”3″ name=”ddgmover” relax_bound=”false” repack_bound=”false” repack_unbound=”false” scorefxn=”fa_score12″ task_operations=”rrf_pack”/>

        </MOVERS>

        <FILTERS>

                <DdGScan ddG_mover=”ddgmover” name=”alascan” repeats=”1″ report_diffs=”1″ scorefxn=”fa_score12″ task_operations=”rrf” write2pdb=”1″/>

        </FILTERS>

        <MOVERS>

                <ReportToDB batch_description=”score12″ name=”3HFM246″>

                        <ResidueFeatures/>

                        <PdbDataFeatures/>

                        <ScoreTypeFeatures/>

                        <ScoreFunctionFeatures scorefxn=”fa_score12″/>

                        <StructureScoresFeatures scorefxn=”fa_score12″/>

                        <ResidueScoresFeatures scorefxn=”fa_score12″/>

                        <DdGFeatures ddG_scan_mover=”alascan”/>

                </ReportToDB>

        </MOVERS>

        <APPLY_TO_POSE/>

        <PROTOCOLS>

                <Add mover_name=”3HFM246″/>

        </PROTOCOLS>

        <OUTPUT/>

</ROSETTASCRIPTS>

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015

core.scoring.etable: Starting energy table calculation

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

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

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

core.scoring.etable: Finished calculating energy tables.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

core.scoring.etable: Starting energy table calculation

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

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

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

core.scoring.etable: Finished calculating energy tables.

basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine

basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt

basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt

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

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

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

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

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

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

core.scoring.utils: [ ERROR ] **********************************************

core.scoring.utils: [ ERROR ] To use the ‘talaris2014’ score function

core.scoring.utils: [ ERROR ] please use the

core.scoring.utils: [ ERROR ]

core.scoring.utils: [ ERROR ]         -restore_talaris_behavior

core.scoring.utils: [ ERROR ]

core.scoring.utils: [ ERROR ] flag on the command line.

core.scoring.utils: [ ERROR ]

core.scoring.utils: [ ERROR ] (And do not use the -restore_pre_talaris_2013_behavior flag.)

our options, or rename the weights file.

Error: [ ERROR ] Exception caught by rosetta_scripts application:

File: src/protocols/parser/ScoreFunctionLoader.cc:77

Weights talaris2014 was requested with incompatible options.

Error: [ ERROR ]

                                

 

 

 

 

[Anonymous]

As the error message says, if you wish to use any of the talaris scorefunctions, you’ll need to add the -restore_talaris_behavior option to the command line. The talaris score functions are incompatible with the settings needed for the current default scorefunction (REF2015).

However,  the settings for talaris score functions are incompatible with the score12 scorefunction. To use the score12 scorefunction, you’ll want to add the -restore_pre_talaris_2013_behavior option. (But this is incompatible with the talaris scorefunctions.)

Unfortunately, there’s no way currently to have both talaris and score12 scoring happening in the same RosettaScript. You’ll either have to convert all the uses of score12 into usage of talaris2013 or talaris2014, convert all the talaris usage into score12 compatible usage, or convert both to use their REF2015 equivalents.

[Anonymous]

.

[Author]

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