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Bug #4482

open

Prep job for Frealign fails

Added by Giovanna Scapin about 8 years ago. Updated about 8 years ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
09/30/2016
Due date:
% Done:

0%

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

Description

With the following message:
Step 3B: from original stack create a new stack file with binning and filtering ready for processing
Traceback (most recent call last):
File "/opt/myamisnap/bin/prepRefineFrealign.py", line 260, in <module>
app.start()
File "/opt/myamisnap/lib/appionlib/apPrepRefine.py", line 420, in start
self.__processStack(prepdata)
File "/opt/myamisnap/lib/appionlib/apPrepRefine.py", line 358, in __processStack
self.preprocessStack()
File "/opt/myamisnap/bin/prepRefineFrealign.py", line 84, in preprocessStack
self.getStackRunParams()
File "/opt/myamisnap/bin/prepRefineFrealign.py", line 77, in getStackRunParams
self.stackrunlogparams = apScriptLog.getScriptParamValuesFromRunname(stackrun['stackRunName'],stackdata['path'],jobdata=None)
File "/opt/myamisnap/lib/appionlib/apScriptLog.py", line 25, in getScriptParamValuesFromRunname
program = getScriptProgramRunFromRunname(runname,pathdata, jobdata)
File "/opt/myamisnap/lib/appionlib/apScriptLog.py", line 17, in getScriptProgramRunFromRunname
apDisplay.printError('No ScriptProgramRun is found for runname %s' % (runname))
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 *
No ScriptProgramRun is found for runname stack42

Thanks - Giovanna

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 #1

Updated by Sargis Dallakyan about 8 years ago

Hi Giovanna, can you please copy the command, working directory or the session name here. I can have a look at that and see what's causing this error.

Thanks - Sargis

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 #2

Updated by Giovanna Scapin about 8 years ago

Hi Sargis
this was run from the APPION interface, session is 16sep09g and the commands + log files are in /gpfs/appion/gscapin/16sep09g/recon/frealign_recon2. This was run from Guppy; there is also a /gpfs/appion/gscapin/16sep09g/recon/frealign_recon1 where I initially tried running it from SEMC-head.

Thanks!

Giovanna

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 #3

Updated by Sargis Dallakyan about 8 years ago

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