Task 1584065622

Stderr output

<core_client_version>7.16.11</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_beta_6.06_windows_x86_64.exe @SETDB1_6BHE_fulldb_ucyRgD_7_5452.flags -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937
Using database: database_f5ae1de8e1\database
Starting watchdog...
Watchdog active.

[ ERROR ]: Caught exception:


File: src/protocols/rosetta_scripts/RosettaScriptsParser.cc:1208
Input rosetta scripts XML file "input_SETDB1_6BHE_fulldb_ucyRgD_7_5452/dock.xml" failed to validate against the rosetta scripts schema. Use the option -parser::output_schema <output filename> to output the schema to a file to see all valid options.
Your XML has failed validation.  The error message below will tell you where in your XML file the error occurred.  Here's how to fix it:

1) If the validation fails on something obvious, like an illegal attribute due to a spelling error (perhaps you used scorefnction instead of scorefunction), then you need to fix your XML file.
2) If you haven't run the XML rewriter script and this might be pre-2017 Rosetta XML, run the rewriter script (tools/xsd_xrw/rewrite_rosetta_script.py) on your input XML first.  The attribute values not being in quotes (scorefunction=talaris2014 instead of scorefunction="talaris2014") is a good indicator that this is your problem.
3) If you are a developer and neither 1 nor 2 worked - email the developer's mailing list or try Slack.
4) If you are an academic or commercial user - try the Rosetta Forums https://www.rosettacommons.org/forum




File: src/protocols/rosetta_scripts/RosettaScriptsSchemaValidator.cc:89
If you are seeing this message, the internally-generated XML Schema for rosetta_scripts could not be properly generated
This failure occurred before your XML script that provided was examined. The error has been compiled into Rosetta and will need to be fixed by a developer.Global schema validation error:  read the error message(s) below and fix your schema in the C++ code.

Errors: Error: Memory allocation failed : xmlSAX2Characters

44832: <xs:complexType name="mover_ParatopeEpitopeConstraintMover_type" mixed="true">
44833:  <xs:annotation><xs:documentation xml:lang="en">
44834:   Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com)
44835: Adds SiteConstraints from the Antibody Paratope to the Epitope on the antigen. Individual residues of the paratope can be set, or specific CDRs of the paratope can be set as well. The Epitope is auto-detected within the set interface distance, unless epitope residues are specified. These SiteConstraints help to keep only the paratope in contact with the antigen epitope (as apposed to the framework or other parts of the antigen) during rigid-body movement. See the Constraint File Overview for more information on manually adding SiteConstraints. Do not forget to add the atom_pair_constraint term to your scorefunction. A weight of .01 for the SiteConstraints seems optimum. Default paratope is defined as all 6 CDRs (or 3 if working with a camelid antibody).
44836:  </xs:documentation></xs:annotation>
44837:  <xs:attribute name="paratope_cdrs" type="xs:string">
44838:   <xs:annotation><xs:documentation xml:lang="en">
44839:    Specifically set the paratope as these CDR.
44840: List of CDR regions (string) devided by one of the following characters: ":,'`~+*|;. "Recognized CDRs: "Aroop|Chothia|Kabat|Martin|North|"
44841:    </xs:documentation></xs:annotation>
44842:  </xs:attribute>
Error: Extra content at the end of the document

44832: <xs:complexType name="mover_ParatopeEpitopeConstraintMover_type" mixed="true">
44833:  <xs:annotation><xs:documentation xml:lang="en">
44834:   Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com)
44835: Adds SiteConstraints from the Antibody Paratope to the Epitope on the antigen. Individual residues of the paratope can be set, or specific CDRs of the paratope can be set as well. The Epitope is auto-detected within the set interface distance, unless epitope residues are specified. These SiteConstraints help to keep only the paratope in contact with the antigen epitope (as apposed to the framework or other parts of the antigen) during rigid-body movement. See the Constraint File Overview for more information on manually adding SiteConstraints. Do not forget to add the atom_pair_constraint term to your scorefunction. A weight of .01 for the SiteConstraints seems optimum. Default paratope is defined as all 6 CDRs (or 3 if working with a camelid antibody).
44836:  </xs:documentation></xs:annotation>
44837:  <xs:attribute name="paratope_cdrs" type="xs:string">
44838:   <xs:annotation><xs:documentation xml:lang="en">
44839:    Specifically set the paratope as these CDR.
44840: List of CDR regions (string) devided by one of the following characters: ":,'`~+*|;. "Recognized CDRs: "Aroop|Chothia|Kabat|Martin|North|"
44841:    </xs:documentation></xs:annotation>
44842:  </xs:attribute>

Warnings: 


 ------------------------ Begin developer's backtrace ------------------------- 
BACKTRACE:
 ------------------------- End developer's backtrace -------------------------- 
DummyMover::apply() should never have been called! (JobDistributor/Parser should have replaced DummyMover.)

ERROR: Function not implemented.
ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 101
02:24:51 (15776): called boinc_finish(0)

</stderr_txt>
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