RosettaCM hybridize mover error after fragment picking

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    • September 6, 2018 at 6:03 pm #2995
      Anonymous

        Hi all,

        I am trying to do some comparitive modeling with RosettaCM by folowing the instructions here https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM

        After fixing a few incorrect (apparently) hardcoded paths in the setup_RosettaCM.py, I can get the rosetta/main/source/bin/rosetta_scripts.static.linuxgccrelease application to run correctly all the way through the “BEGIN MOVER Hybridize – hybridize” and fragment picking steps. However, the program then quits after multiple errors as showin in the log fragment below…

        A log of the full std out and std error is attached. 

        If anyone can helpme fix this error I’d be most appreciative. 

        Thanks.

        -Andrew 


        
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Hybridize - hybridize=======================
        
core.fragment.picking_old.vall.vall_io: Reading Vall library from /home/ubuntu/rosetta/main/database//sampling/filtered.vall.dat.2006-05-05 ...
        
core.fragment.picking_old.vall.vall_io:    100000
        
core.fragment.picking_old.vall.vall_io:    200000
        
core.fragment.picking_old.vall.vall_io:    300000
        
core.fragment.picking_old.vall.vall_io:    400000
        
core.fragment.picking_old.vall.vall_io:    500000
        
core.fragment.picking_old.vall.vall_io:    600000
        
core.fragment.picking_old.vall.vall_io:    700000
        
core.fragment.picking_old.vall.vall_io:    800000
        
core.fragment.picking_old.vall.vall_io:    900000
        
core.fragment.picking_old.vall.vall_io:    1000000
        
core.fragment.picking_old.vall.vall_io:    1100000
        
core.fragment.picking_old.vall.vall_io:    1200000
        
core.fragment.picking_old.vall.vall_io:    1300000
        
core.fragment.picking_old.vall.vall_io:    1400000
        
core.fragment.picking_old.vall.vall_io: ... done.  Read 1400124 lines.  Time elapsed: 8 seconds.
        
core.fragment.picking_old.vall.vall_io: Prior library contained 0 sections totaling 0 residues.
        
core.fragment.picking_old.vall.vall_io: Added 62471 sections to library totaling 1400124 residues.
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = NDHRYRRFT
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00059
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 5.00002
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = DHRYRRFTQ
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 4.00001
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 5.00003
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = HRYRRFTQL
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 4.00003
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00075
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = RYRRFTQLP
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00079
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00047
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = YRRFTQLPN
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00019
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.0007
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = RRFTQLPNG
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00038
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00033
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = RFTQLPNGR
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00019
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00034
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = FTQLPNGRD
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00008
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00039
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = TQLPNGRDY
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00064
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.0004
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = QLPNGRDYH
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00024
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00058
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = LPNGRDYHY
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00086
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00068
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = PNGRDYHYS
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00016
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00054
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = NGRDYHYSV
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00001
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00067
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = GRDYHYSVV
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00059
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00044
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = RDYHYSVVG
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00058
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.0008
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = DYHYSVVGP
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 4
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00055
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = YHYSVVGPE
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00048
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00042
        
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = HYSVVGPED
        
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00006
        
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00043
        
protocols.hybridization.HybridizeProtocol: FRAGMENTS small max length: 3
        
protocols.hybridization.HybridizeProtocol: FRAGMENTS big max length: 9
        

        
ERROR: Assertion `weights_.size()` failed.
        
ERROR:: Exit from: src/numeric/random/WeightedSampler.cc line: 118
        
BACKTRACE:
        
[0x58c6188]
        
[0x574ee59]
        
[0x1131fdb]
        
[0x1132354]
        
[0x3544771]
        
[0x354593b]
        
[0x35460be]
        
[0x35aa058]
        
[0x35abb61]
        
[0x364e6d8]
        
[0x410acb]
        
[0x5e0bee4]
        
[0x6151fd]
        
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:
        

        
File: src/numeric/random/WeightedSampler.cc:118
        
[ ERROR ] UtilityExitException
        
ERROR: Assertion `weights_.size()` failed.
        

        

        
protocols.jd2.JobDistributor: [ ERROR ]
        

        
[ERROR] Exception caught by JobDistributor for job S_0001
        

        
File: src/numeric/random/WeightedSampler.cc:118
        
[ ERROR ] UtilityExitException
        
ERROR: Assertion `weights_.size()` failed.
        

        

        
protocols.jd2.JobDistributor: [ ERROR ]
        
protocols.jd2.JobDistributor: [ WARNING ] S_0001 reported failure and will NOT retry
        
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Hybridize - hybridize=======================
        
protocols.hybridization.HybridizeProtocol: FRAGMENTS small max length: 3
        
protocols.hybridization.HybridizeProtocol: FRAGMENTS big max length: 9
        

        
ERROR: Assertion `weights_.size()` failed.
        
ERROR:: Exit from: src/numeric/random/WeightedSampler.cc line: 118
        
BACKTRACE:
        
[0x58c6188]
        
[0x574ee59]
        
[0x1131fdb]
        
[0x1132354]
        
[0x3544771]
        
[0x354593b]
        
[0x35460be]
        
[0x35aa058]
        
[0x35abb61]
        
[0x364e6d8]
        
[0x410acb]
        
[0x5e0bee4]
        
[0x6151fd]
        
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:
        

        
File: src/numeric/random/WeightedSampler.cc:118
        
[ ERROR ] UtilityExitException
        
ERROR: Assertion `weights_.size()` failed.

         

        UPDATE:

        The apparently same error occurs on a macOS install too. The error logs may be somewhat more informative and are attached. 

         

         

      • December 26, 2019 at 6:22 pm #15103
        Anonymous

          I had a same problem. –> “ERROR: Assertion `weights_.size()` failed.”

           

          It turned out that I didn’t specify

          <Template pdb=”~~.pdb” weight=”~~” />

          in my rosetta_script xml.

           

          Once I specified it, I ran successfully.

        • December 26, 2019 at 6:23 pm #15102
          Anonymous

            (does anyone know how to erase the my reply?)

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