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ID | Project | Category | View Status | Date Submitted | Last Update | ||||
0000231 | Rosetta | [All Projects] Incorrect Results | public | 2013-03-25 12:36 | 2013-04-04 11:08 | ||||
Reporter | jecorn | ||||||||
Assigned To | mtyka | ||||||||
Priority | normal | Severity | minor | Reproducibility | always | ||||
Status | resolved | Resolution | no change required | ||||||
Platform | All platforms | OS | Any | OS Version | Any | ||||
Product Version | Trunk | ||||||||
Fixed in Version | Trunk | ||||||||
Summary | 0000231: -out:user_tag option only sometimes obeyed | ||||||||
Description | The -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 Reproduce | Run 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). | ||||||||
Tags | jd2, silent files | ||||||||
Application(s) Affected | rosetta_scripts | ||||||||
Command Line Used | rosetta_scripts.linuxgccrelease -out:file:silent_struct_type binary -out:file:silent out.out | ||||||||
Developer Options | |||||||||
Fixed in SVN Version | - | ||||||||
Attached Files | |||||||||
Relationships | |||||||||||
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Notes | |
(0000248) mtyka (Developer) 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 (Developer) 2013-04-04 01:59 |
Working as intended. Correct option to modify decoy_tag is -out::prefix and -out::suffix |
Issue History | |||
Date Modified | Username | Field | Change |
2013-03-25 12:36 | jecorn | New Issue | |
2013-03-25 12:36 | jecorn | Status | new => assigned |
2013-03-25 12:36 | jecorn | Assigned To | => smlewis |
2013-03-25 12:37 | jecorn | Tag Attached: jd2 | |
2013-03-25 12:37 | jecorn | Tag Attached: silent files | |
2013-04-04 01:52 | mtyka | Assigned To | smlewis => mtyka |
2013-04-04 01:55 | mtyka | Developer Options | Confirmed As Bug => |
2013-04-04 01:55 | mtyka | Note Added: 0000248 | |
2013-04-04 01:55 | mtyka | Resolution | open => no change required |
2013-04-04 01:59 | mtyka | Fixed in SVN Version | => - |
2013-04-04 01:59 | mtyka | Note Added: 0000249 | |
2013-04-04 01:59 | mtyka | Status | assigned => resolved |
2013-04-04 01:59 | mtyka | Fixed in Version | => Trunk |
2013-04-04 11:05 | jecorn | Relationship added | related to 0000243 |
2013-04-04 11:08 | jecorn | Relationship added | related to 0000244 |
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