Project

General

Profile

Actions

Bug #4052

open

Xmipp projection matching refinement does not work

Added by Christoph Wigge over 8 years ago. Updated over 8 years ago.

Status:
In Test
Priority:
High
Category:
Image Processing
Target version:
-
Start date:
03/21/2016
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:

Description

When running xmipp the prepare stack functions seems to work and then the run finishes but when I would like to upload the results it complains with following error

.. Time stamp: 16mar21p00
... Function name: uploadXmippRefine
... Appion directory: /opt/myamisnap/lib
... Processing hostname: guppy-18
... Using split database
Connected to database: 'nyap_20'
... Committing data to database
!!! WARNING: recon dir already exist, no need to unpack
... Getting stack data for stackid=122
Old stack info: 'xmipp stack combine ... combined stack ids 121,119,118,117'

!!! WARNING: timestamp could not be found from the jobdata
uploading refinement results for Xmipp reconstruction routine
... Getting stack data for stackid=122
Old stack info: 'xmipp stack combine ... combined stack ids 121,119,118,117'

... Mapping 49673 stack particle IDs
... Mapped 49673 stack particle IDs in 358.39 msec
... Run directory: /gpfs/appion/cwigge/15dec11c/recon/xmipp_recon3
!!! WARNING: directory '/gpfs/appion/cwigge/15dec11c/recon/xmipp_recon3' already
exists.
... Writing function log to: uploadXmippRefine.log
... Uploading ScriptData....
... Found 1 processors on this machine
... Running Appion version 'myami-3.2'
... Xmipp ran 1 iterations
Traceback (most recent call last):
File "/opt/myamisnap/bin/uploadXmippRefine.py", line 490, in
upload3D.start()
File "/opt/myamisnap/bin/uploadXmippRefine.py", line 441, in start
uploadIterations = self.verifyUploadIterations(lastiter)
File "/opt/myamisnap/lib/appionlib/reconUploader.py", line 322, in verifyUploadIterations
"--uploadIterations=1,2,3,4,5,6,7,8" % (self.package, lastiter, self.runparams['numiter']))
File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 65, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception:
  • FATAL ERROR ***
    Xmipp job did not go to completion. The last completed iteration is 1, out of 10 specified. Please s
    ... terations=1,2,3,4,5,6,7,8
Actions

Also available in: Atom PDF