How to recover out files when run crashs

Member Site Forums Rosetta 3 Rosetta 3 – General How to recover out files when run crashs

Viewing 1 reply thread
  • Author
    • #2240

        Dear users,
        I’d tried to run 50 000 models from ab initio Rosetta protocol using the options bellow [1]. After running some models my ab initio crashed due to problems with eletric supplies. I reinitiated the ab initio protocol intendind to generate my 50 000 models and I guess: if I’m very interested to analyse the “inital models” (that ones that was generated until the ab initio crashed), how can I “recover” these information from my out file until its crashed?
        Afterwards I tried to extract the score data [2] from my out file after crash and the program give me this answer [3]. Somebody has any tips?

        [1] Ab initio protocol:
        -database /home/guest/rosetta/rosetta_database
        -in:file:fasta /home/guest/Documents/lais/bamil/novosfragmentosdabamil/bamil2comhomologos/t000_.fasta
        -in:file:frag3 /home/guest/Documents/lais/bamil/novosfragmentosdabamil/bamil2comhomologos/aat000_03_05.200_v1_3
        -in:file:frag9 /home/guest/Documents/lais/bamil/novosfragmentosdabamil/bamil2comhomologos/aat000_09_05.200_v1_3
        -use_filters true
        -out:file:silent bamil2_50k.out
        -nstruct 50000
        -jran 1234567
        -psipred_ss2 /home/guest/Documents/lais/bamil/novosfragmentosdabamil/bamil2comhomologos/t000_.psipred
        -abinitio::increase_cycles 10
        -abinitio::rsd_wt_helix 0.7
        -abinitio::rg_reweight 0.5
        -seed_offset 10

        [2] Score command line
        score.linuxgccrelease -database /home/guest/rosetta/rosetta_database -in:file:fullatom -in:file:silent bamil2_50k.out -out:pdb -out:file:silent 2.out -relax:fast -out:output -out:file:scorefile -in:file:native 1IYT.pdb

        [3] Score Error
        core.init: Mini-Rosetta version Split from developer trunk at 53488 from
        core.init: command: score.linuxgccrelease -database /home/guest/rosetta/rosetta_database -in:file:fullatom -in:file:silent bamil2_50k.out -out:pdb -out:file:silent 2.out -relax:fast -out:output -out:file:scorefile -in:file:native 1IYT.pdb
        core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-834711011 seed_offset=0 real_seed=-834711011
        core.init.random: RandomGenerator:init: Normal mode, seed=-834711011 RG_type=mt19937
        Rosetta Tool: score – rescores PDBs and silent files, extracts PDBs from silent files, assembles PDBs into silent files.
        PDB input: -in:file:s *.pdb or
        -in:file:l list_of_pdbs
        -no_optH Dont change positions of Hydrogen atoms! (default true, specify false if you want optH)
        Silent input: -in:file:silent silent.out silent input filesname
        -in:file:tags specify specific tags to be extracted, if left out all will be taken
        -in:file:fullatom for full atom structures
        -in:file:binary_silentfile for non-ideal structures (such as from looprelax)
        -in:file:silent_optH Call optH when reading silent files (useful for HisD/HisE determination)
        -score_app:linmin Run a quick linmin before scoring
        Native: -in:file:native native PDB (rms, maxsub and gdtm scores will be calculated)
        Scorefunction: -score:weights weights weight set or weights file
        -score:patch patch patch set
        -score:optH_weights Weights file for optH (default standard.wts w/ sc12 patch)
        -score:optH_patch Weights patch file for optH
        -rescore:verbose display score breakdown
        Output: -out:nooutput don’t print PDB structures (default now)
        -out:output force printing of PDB structures
        -out:file:silent write silent-out file
        -out:file:scorefile name write scorefile (default
        -out:prefix myprefix prefix the output structures with a string
        score -database ~/minirosetta_database -in:file:silent silent.out -in::file::binary_silentfile -in::file::fullatom -native 1a19.pdb
        Will rescore all structures in silent.out, in full atom mode and accounting for nonideal structure if present. Additionally
        it will print a PDB for every structure with -out:output flag
        core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
        core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
        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. Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
        *** renamed tag S_00019682 to S_00019682_3 (SilentStruct with S_00019682 already exists!) renamed tag S_00019711 to S_00019711_1 (SilentStruct with S_00019711 already exists!) renamed tag S_00019712 to S_00019712_1 (SilentStruct with S_00019712 already exists!) renamed tag S_00019698 to S_00019698_2 (SilentStruct with S_00019698 already exists!) renamed tag S_00019683 to S_00019683_3 (SilentStruct with S_00019683 already exists!) renamed tag S_00019699 to S_00019699_2 (SilentStruct with S_00019699 already exists!) renamed tag S_00019713 to S_00019713_1 (SilentStruct with S_00019713 already exists!) renamed tag S_00019684 to S_00019684_3 (SilentStruct with S_00019684 already exists!) renamed tag S_00019700 to S_00019700_2 (SilentStruct with S_00019700 already exists!) renamed tag S_00019685 to S_00019685_3 (SilentStruct with S_00019685 already exists!) renamed tag S_00019714 to S_00019714_1 (SilentStruct with S_00019714 already exists!) renamed tag S_00019701 to S_00019701_2 (SilentStruct with S_00019701 already exists!) renamed tag S_00019715 to S_00019715_1 (SilentStruct with S_00019715 already exists!) renamed tag S_00019686 to S_00019686_3 (SilentStruct with S_00019686 already exists!) renamed tag S_00019702 to S_00019702_2 (SilentStruct with S_00019702 already exists!) renamed tag S_00019716 to S_00019716_1 (SilentStruct with S_00019716 already exists!) renamed tag S_00019687 to S_00019687_3 (SilentStruct with S_00019687 already exists!) renamed tag S_00019703 to S_00019703_2 (SilentStruct with S_00019703 already exists!) renamed tag S_00019717 to S_00019717_1 (SilentStruct with S_00019717 already exists!) renamed tag S_00019688 to S_00019688_2 (SilentStruct with S_00019688 already exists!) ERROR: !is_int( ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@SCORE: ) from line (^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@SCORE: -62.140 -128.320 16.276 55.506 0.390 0.000 -1.199 -7.509 -7.832 -3.792 0.000 0.000 0.000 0.000 0.000 -0.402 2.926 20.512 -4.566 -4.130 0.000 0.000 0.000 0.000 10.046 0.000 0.000 185.000 S_00019727) Are you trying to read a binary silent file ? Use -in:file:silent_struct_type binary

      • #11114

          You probably want to include the flag “-silent_read_through_errors” in your scoring run. That should skip over the incomplete structure made during the powercut.

        • #11119

            Thanks rmoretti. It’s works!

        Viewing 1 reply thread
        • You must be logged in to reply to this topic.