Suppress printing to STDOUT for applications

[Anonymous]

 

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

[Anonymous]

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.

[Anonymous]

 

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

 

[Anonymous]

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.

score -in:file:silent silent.out -in::file::binary_silentfile -in::file::fullatom -native 1a19.pdb > /dev/null

 

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.)

[Anonymous]

 

Thanks!

 

 

[Anonymous]

Hello rmoretti,

Would I miss any important information (like the errors messages, etc.), if I use ‘-mute all’? Thank you!

[Author]

Posts