docking parse error

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    • December 4, 2018 at 4:41 pm #3048
      Anonymous

        Hello,

        I’m trying to use the highres docking protocol  with rosetta3.9 and I still get this error (see below), no matter what I do with the xml protocol (attached):

        I would appreciate any suggestion

        best regards,

        Dave

        The command I run:

        rosetta_scripts.static.linuxgccrelease -in:file::s 1mj5.pdb -parser:protocol docking.xml -extra_res_fa r_lig.params

         

        rotocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=docking.xml

        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

        Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job ‘1mj5_0001’

        Error: [ ERROR ]

        File: src/utility/tag/Tag.cc:557

        Tag::read – parse error, printing backtrace.

        Tag::read – parse error – file:istream line:1 column:1 – <ROSETTASCRIPTS>

        Tag::read – parse error – file:istream line:1 column:1 – ^

        Error: [ ERROR ]

        Error: [ ERROR ] Treating failure as bad input; canceling similar jobs

        protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: 1mj5_0001

        protocols.jd2.JobDistributor: no more batches to process…

        protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 19 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 ]

         

      • December 4, 2018 at 4:55 pm #14524
        Anonymous

          That’s very, very strange. Your script passed the validation stage (which is where syntax errors should be caught), but wasn’t able to be parsed.

          If I had to guess, I’d say that there’s some sort of odd whitespace in the XML which the validator is fine with, but the parser is choking on.

          My first recommendation is to run your XML through the dos2unix program. This should fix up some common line ending issues which sometimes cause Rosetta to choke (I haven’t seen it happen here, though).

          If that doesn’t work, you can try the following command: 


          
tr -cd '111240-176' < input.xml > cleaned.xml

          where “input.xml” is your current XML file, and “cleaned.xml” is a name for the fixed file. (Note that the less than and greater than signs in the command should be typed on the commandline.)  Be sure to open the cleaned.xml in a text editor to make sure everything looks okay. Depending on what things you had going on, you may need to fixup things like quotes, dashes, etc., if you had the “wrong” style of character.

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