Scipion relion - particles extraction

I2PC / scipion

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)

http://scipion.i2pc.es

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Scipion relion - particles extraction #2041

Closed S160024 closed 3 years ago

S160024 commented 5 years ago

Usually when running in Relion 3.0, the particles extracted would result in an output file that can be read for 2D classifications. However, in Scipion, there seems to be an error in producing the output file.

Step 2 in Scipion-relion particles extraction failure. The particles extractions was performed properly, however, the output file is not available.

Capture

Despite editing the failed process and clicking continue, the error still pops up. Is there a bug issue or is there a coding issue? I'm currently running on Ubuntu Centos 7.

pconesa commented 5 years ago

Thank you @S160024 , I'm involving here Relion plugin developers

azazellochg commented 5 years ago

@S160024 could you provide full output logs, screenshot of protocol parameters used so we could reproduce it? Also, are you running extraction in streaming or not? Also, which relion plugin version are you using?

delarosatrevin commented 5 years ago

From the shown error trace, it seems to be in streaming...still will be good to have full logs and parameters.

azazellochg commented 5 years ago

@S160024 any update on this?

S160024 commented 5 years ago

Hi there sorry for the late response.

The full log file is attached. run.log

The parameters used is the coordinates from relion's autopicking LoG output file The micrograph source are from xmipp3-ctf consensus output file. The particle box size is 150 px, with no rescale of particles.

The preprocess parameters are as follows:

no invert contrast
no normalise particles.

the streaming was set as 0 seconds sleep when waiting and 0 batch size.

azazellochg commented 5 years ago

Thanks, @S160024, we'll try to reproduce it. Could you also attach run.stdout which is more detailed?

S160024 commented 5 years ago

Hi @azazellochg , I'm unable to attach it. However, i've uploaded on dropbox and you may access the run.stdout file in the link below.

https://www.dropbox.com/s/j1oiwlhdktp5i80/run.stdout?dl=0

JuhaHuiskonen commented 4 years ago

For me 'relion - particle extraction' is also failing when I try to extract using coordinates from 'relion - auto-picking LoG' in streaming mode

azazellochg commented 4 years ago

Confirmed as a bug in core extraction protocol

pconesa commented 4 years ago

Thanks @azazellochg , have you manage to reproduce it. Since test are passing, I guess there must be a specific condition that makes it fail and test are not covering? I guess we can assign it to us.

azazellochg commented 4 years ago

I was able to reproduce it in cistem since I copied the relion code from that protocol to cistem picker.

azazellochg commented 3 years ago

This is definitely fixed.