You are here

JD3 w/ Silent file output crashing - Option filename not found

3 posts / 0 new
Last post
JD3 w/ Silent file output crashing - Option filename not found
<Job nstruct="5">
          <PDB filename="pdb_basename.pdb" />
          <SilentFile path="pdb_basename" filename="pdb_basename_relaxed.silent"  />
          <ScoreFile path="pdb_basename" filename="" />
          <parser__protocol value="path/to/RELAX_MONOMER_RS" />

Apologies if this is the wrong category, couldn't quite determine which one this best fit into.

I'm using JD3 to run a protocol on multiple input PDBs (for now just FastRelax) and am trying to output all structures for a given input to a single silent file. However, whenever I try this with <Output> set to a silent file as above, Rosetta crashes & I get the following error (I've attached the full crash file as well):

[FILE]: src/utility/tag/Tag.hh
[LINE]: 182
Option filename not found.


When I replace the silent file with <PDB path="pdb_basename" filename_pattern="$_relaxed.pdb" /> the script runs as expected and outputs several relaxed PDBs in the folder pdb_basename; the issue just seems constrained to using SilentFiles, but I can't figure out the issue just based on the JD3 documentation (

Thanks in advance for the help! Happy to provide more info as needed as well



Post Situation: 
Mon, 2023-10-30 13:40

This looks to be a bug with Silent File output. Looking at the code, for some reason it's attempting to look for the filename attribute on the Output tag, rather than the SilentFile tag. But the XML validation doesn't allow there to be a filename tag on the Output tag.

I would recommend either using PDB output, or seeing if you can use the JD2 version of RosettaScripts instead.

Mon, 2023-10-30 14:06

Thanks for the quick response! I'll probably just go with PDB output for now - definitely not a gamebreaker - and might just write a quick script to compile them into a silent file after the fact.

Is there a bug tracker/similar to report this on, or is this the main place for that? Tried to check out but that seems to be down.

Mon, 2023-10-30 15:35