Bug #1461
closedPost processing is not working anymore
0%
Description
I ran a Xmipp refinement and uploaded it to the database. Postprocessing dies with this error message
... Time stamp: 11nov10i14... Function name: postProc
... Appion directory: /opt/myamisnap/lib
... Load average is high 2.03
!!! WARNING: Using split database
Connected to database: 'ap341'
... Committing data to database
Traceback (most recent call last):
File "/opt/myamisnap/bin/postProc.py", line 309, in ?
postProc = PostProcScript()
File "/opt/myamisnap/lib/appionlib/appionScript.py", line 83, in init
self.checkConflicts()
File "/opt/myamisnap/bin/postProc.py", line 98, in checkConflicts
self.params['fscfile'] = self.getFscFile()
File "/opt/myamisnap/bin/postProc.py", line 178, in getFscFile
apDisplay.printError("failed to find fscfile: "+fscfile)
File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 57, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception:
- FATAL ERROR ***
failed to find fscfile: /ami/data00/appion/11oct11d/recon/xmipp_recon24-C1/Xmipp_results/iter012/fsc.eotest.12
Updated by Anchi Cheng over 12 years ago
Arne,
Neither Amber nor I have gone that far down in processing to have done anything for post processing after the recon refactoring, yet. You will either have to wait or, as Amber called, "muscle it through" and commit the changes.
Updated by Arne Moeller over 12 years ago
I used this command:
[moeller@amibox03 refine23_11nov10i13]$ cat refine23_11nov10i13.appionsub.job
#!/bin/csh
#PBS -l walltime=240:00:00
#PBS -l nodes=1:ppn=1
#PBS -m e
#PBS -j oe
updateAppionDB.py 200 R 341
webcaller.py '/opt/myamisnap/bin/appion postProc.py --reconiterid=23 -s 11oct11d -f /ami/data00/appion/11oct11d/recon/xmipp_recon24-C1/Xmipp_results/recon_11nov08o21_it012_vol001.mrc --bfactor --apix=1.3760673333333 --res=15.45 --sym=c1 --median=2 --zoom=1.0 --contour=2.0 --lp=7.73 --norm --rundir=/ami/data00/appion/11oct11d/recon/xmipp_recon24-C1/Xmipp_results/postproc/refine23_11nov10i13 --runname=refine23_11nov10i13 --projectid=341 --expId=9124 ' /ami/data00/appion/11oct11d/recon/xmipp_recon24-C1/Xmipp_results/postproc/refine23_11nov10i13/refine23_11nov10i13.appionsub.log
updateAppionDB.py 200 D 341
exit
Updated by Amber Herold over 12 years ago
- Status changed from New to Assigned
- Assignee set to Amber Herold
- Priority changed from Normal to High
- Target version set to Appion/Leginon 2.2.0
- Affected Version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.2.0 (trunk)
Updated by Amber Herold over 12 years ago
- Status changed from Assigned to In Code Review
- Assignee changed from Amber Herold to Anchi Cheng
Fixed the fsc file issue.
After the recon refactor, results are copied to the local file server and unzipped into a directory called recon. Then those files are translated into what we need to be able to upload into Appion and the new files are stored in a folder called "Method_results" where "Method" is Xmipp or EMAN or whatever else is being used. Both the path to this new results folder and the name of the masssaged fsc file are stored in the database.
To fix the bug we simply look up the path and file name in the database, rather than constructing the path and filename for the specific methods results as we used to do.
Please assign to Arne to test.
Updated by Anchi Cheng over 12 years ago
- Status changed from In Code Review to In Test
- Assignee changed from Anchi Cheng to Arne Moeller
Updated by Amber Herold about 12 years ago
Arne, will you be able to test this in the next few days? I want to close out high priority tests (more recently added code) prior to 2.2 release.