HI,
Is there an option to suppress the printing to STDOUT for applications? Specifically, I'd like to run fixbb and the score app silently in Rosetta 3.5.
Thanks
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You want "-mute all". This turns off almost all output, except for a little bit that occurs at the beginning. You can also redirect output to /dev/null to completely obliterate it.
"all" is a special argument to -mute, but it accepts any tracer names. Tracers are the hierarchical tags prepended onto each line (the bits at the beginning, that say stuff like core.pack.task:). So you could do "-mute core.pack" or whatever to silence only some of the output.
Thanks!
However, I'm still getting this output for the score application when using "-mute all":
#######################################################################################
Rosetta Tool: score - rescores PDBs and silent files, extracts PDBs from silent files, assembles PDBs into silent files .
Usage:
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 default.sc)
-out:prefix myprefix prefix the output structures with a string
Examples:
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
############################################################################################
Is there anyway to suppress this as well (using a flag within the initial rosetta score command)?
Thanks
The '-mute all' will only affect things that go through the Rosetta tracer system. Certain output (some usage commands, some error messages) doesn't go through the tracer system, and so won't be affected by it. In general, no option controls that output.
Instead, you'll need to use the redirect to /dev/null that Steven mentioned. e.g.
Note that this isn't Rosetta specific. Instead, it's using the native Linux output redirection tools to redirect the output to a file-like object which will just drop all the text. This is really the only way to completely supress Rosetta output. (Though depending on your protocol, the '-mute all' option normally will work too.)
Thanks!
Hello rmoretti,
Would I miss any important information (like the errors messages, etc.), if I use '-mute all'? Thank you!