Appion

Arne, r17112 contains all the pieces for the prep step. You should be able to create the prep command from the web page and run the prepRefineRelion.py file. I have NOT made changes to the python file to remove the stack inversion step and add the awk command.

r17113 includes the form for the run step. Still need to write the python class for the run step.

Neil has made changes. Neil will upload his changes to trunk. Kids will test.

An error was reported for this, can I get the error message.

Jana and I have tried to use Relion in the Appion pipeline in December 2014 unsuccessfully.

I had the job prepared (with a template), but when I ran it none of the iterations went through. The directory on fishtail is: /ami/data15/appion/14nov19f/recon/relion_recon1/relion_recon1.appionsub.job

Thank you.

Thank you. I see this in one of the *.o files:

MetaDataTable::read: File /ami/data15/appion/14nov19f/recon/relion_recon1/all_images.star does not exists

MlOptimiserMpi::initialiseWorkLoad: at least 3 MPI processes are required when splitting data into random halves

=>> PBS: job killed: mem job total 5258200 kb exceeded limit 4194304 kb

Bridget will take on testing.