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virtual stacks can't be used for xmipp projection matching in appion #3571

Open leginonbot opened 8 months ago

leginonbot commented 8 months ago

Author Name: Emily Greene (Emily Greene) Original Redmine Issue: 3571, https://emg.nysbc.org/redmine/issues/3571 Original Date: 2015-09-19 Original Assignee: Gabriel Lander

During job preparation for xmipp projection matching, there was the following error (/data2/log-l/appion/15sep10a/recon/xmipp_recon1):

Step 3B: from original stack create a new stack file with binning and filtering ready for processing

['/usr/local/appion/EMAN2/bin', '/data2/log-l/progs/myami/appion', '/usr/local/appion/EMAN2/lib'] Traceback (most recent call last): File "/data2/log-l/progs/myami/appion/bin/prepRefineXmipp.py", line 29, in app.start() File "/data2/log-l/progs/myami/appion/appionlib/apPrepRefine.py", line 420, in start self.processStack(prepdata) File "/data2/log-l/progs/myami/appion/appionlib/apPrepRefine.py", line 358, in processStack self.preprocessStack() File "/data2/log-l/progs/myami/appion/appionlib/apPrepRefine.py", line 122, in preprocessStack apDisplay.printError("stackfile does not exist: "+self.stack['file']) File "/data2/log-l/progs/myami/appion/appionlib/apDisplay.py", line 65, in printError raise Exception, colorString("\n FATAL ERROR \n"+text+"\n\a","red") Exception: FATAL ERROR stackfile does not exist: /data2/log-l/appion/15sep10a/stacks/alignsub63/start.hed

Current workaround is to make a new stack from the substack, which generates a start.hed file.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Gabriel Lander (@gclander) Original Date: 2015-09-19T20:25:53Z

I can fix this next week. In the meantime, there should be a button next to any virtual stack that you can use to generate the stack files. You don't have to make a new one from the substack.