MantisBT - Rosetta
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IDProjectCategoryView StatusDate SubmittedLast Update
0000231Rosetta[All Projects] Incorrect Resultspublic2013-03-25 12:362013-04-04 11:08
Reporterjecorn 
Assigned Tomtyka 
PrioritynormalSeverityminorReproducibilityalways
StatusresolvedResolutionno change required 
PlatformAll platformsOSAnyOS VersionAny
Product VersionTrunk 
Fixed in VersionTrunk 
Application(s) Affectedrosetta_scripts
Command Line Usedrosetta_scripts.linuxgccrelease -out:file:silent_struct_type binary -out:file:silent out.out
Developer Options
Fixed in SVN Version-
Summary0000231: -out:user_tag option only sometimes obeyed
DescriptionThe -out:user_tag option is documented as adding a user-generated id to structure tags in silent files. This can be very useful for uniqueifying tags across multiple processes (e.g. adding a process ID), simplifying grepping of structures from the silent files.

This behavior works with some apps and not with others. The minirosetta app can write both text and binary silent files such that the silent files have both a new field called "user_tag" and the user_tag is added to the "description field" (S_<user_tag>_####). However, rosetta_scripts (which solely uses binary silent files) writes silent files with the "user_tag" field, but the user_tag is NOT added to the structure tag.

Both minirosetta and rosetta_scripts use jd2. However, minirosetta uses a specialized BOINCJobDistributor. Is this part of the cause? Or is there something special about the rosetta_scripts silent file handling that forgets to check for user_tag?
Steps To ReproduceRun minirosetta app app "-out:user_tag 1" and either -out:file:silent_struct_type protein (default) or -out:file:silent_struct_type binary. Marvel at the user_tag in the description (S_1_00000001)

Run rosetta_scripts with "-out:user_tag 1" (default/only behavior is -out:file:silent_struct_type binary) and cringe at the lack of user_tag in the description (S_0001).
Additional Information
Tagsjd2, silent files
Relationships
related to 0000243assigned smlewis Incorrect documentation of -out:user_tag option 
related to 0000244assigned smlewis minirosetta app incorrectly uses -out:user_tag option 
Attached Files
Issue History
Date ModifiedUsernameFieldChange
2013-03-25 12:36jecornNew Issue
2013-03-25 12:36jecornStatusnew => assigned
2013-03-25 12:36jecornAssigned To => smlewis
2013-03-25 12:37jecornTag Attached: jd2
2013-03-25 12:37jecornTag Attached: silent files
2013-04-04 01:52mtykaAssigned Tosmlewis => mtyka
2013-04-04 01:55mtykaDeveloper OptionsConfirmed As Bug =>
2013-04-04 01:55mtykaNote Added: 0000248
2013-04-04 01:55mtykaResolutionopen => no change required
2013-04-04 01:59mtykaFixed in SVN Version => -
2013-04-04 01:59mtykaNote Added: 0000249
2013-04-04 01:59mtykaStatusassigned => resolved
2013-04-04 01:59mtykaFixed in Version => Trunk
2013-04-04 11:05jecornRelationship addedrelated to 0000243
2013-04-04 11:08jecornRelationship addedrelated to 0000244

Notes
(0000248)
mtyka   
2013-04-04 01:55   
[working as intended]

Looks like user_tag is behaving as designed - it's not supposed to be added to the tag. It is only supposed to show up as an extra field. If the user_tag is showing up in the decoy_tag in minirosetta app then that's a seperate bug.

The flag you want is -out:prefix (or -out:suffix) and does exactly what you wanted - it modifies the decoy_tag and works just fine in rossetta_scripts.
(0000249)
mtyka   
2013-04-04 01:59   
Working as intended.

Correct option to modify decoy_tag is -out::prefix and -out::suffix