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Mean/StdDev filtering of stack not working with virtual stack #3660

Open leginonbot opened 3 months ago

leginonbot commented 3 months ago

Author Name: Priyamvada Acharya (Priyamvada Acharya) Original Redmine Issue: 3660, https://emg.nysbc.org/redmine/issues/3660 Original Date: 2015-10-14 Original Assignee: Gabriel Lander

Error message:

subStack.start() File "/opt/myamisnap/bin/stackFilter.py", line 88, in start apStack.makeNewStack(oldstack, newstack, self.params['keepfile'], bad=True) File "/opt/myamisnap/lib/appionlib/apStack.py", line 55, in makeNewStack a.run() File "/opt/myamisnap/lib/appionlib/proc2dLib.py", line 45, in run self.approc2d.checkConflicts() File "/opt/myamisnap/lib/appionlib/proc2dLib.py", line 112, in checkConflicts self.inputNumParticles = self.inheader['nz'] TypeError: 'NoneType' object is unsubscriptable

Session ID: 15oct05d Path: /gpfs/appion/pacharya/15oct05d/stacks/alignsub53/

leginonbot commented 3 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2015-10-15T01:00:44Z

The error in /gpfs/appion/pacharya/15oct05d/stacks/meanfilt103

!!! WARNING: could not find old stack: /gpfs/appion/pacharya/15oct05d/stac
ks/alignsub53/start.hed

alignsub53 Ended at Wed, 14 Oct 2015 11:17:50 but the stack modified time was Oct 14 15:00

It seems that the stack in question was not generated until 15:00. The stackFilter.py ran after that worked fine.

Any comment on why the stack was modified after the run ended ? Is this a virtual stack ? Could this be related to virtual stack function ?

leginonbot commented 3 months ago

Original Redmine Comment Author Name: Venkata Dandey (Venkata Dandey) Original Date: 2015-10-15T01:18:36Z

I had the same issue... Actually some times the stack created shows like "generate some missing information" in the place of size of the stack in MB.

So, when I tried to click the "generate some missing information" it shows a command which as I remember starts with something like "generate information". I copied the command and run over the terminal in cluster and then size of the stack showed up.

After this any stack operation worked. Don't know what causing this issue... But there is work around for now. I hope this info helps to debug.

leginonbot commented 3 months ago

Original Redmine Comment Author Name: Gabriel Lander (@gclander) Original Date: 2015-10-15T01:27:49Z

the Mean/STDdev function hasn't been fixed to work with virtual stacks yet. Nor has xmipp projection matching. Unfortunately I haven't had the time to dedicate to this, in the meantime continue with the workaround of generating the stack. Alternatively, when you make a substack, there's a checkbox to make the actual file instead of a virtual stack.