protomo2aligner.py --dose_presets=Moderate --frame_aligned=True --parallel=True --region_x=1919 --region_y=1855 --sampling=8 --map_sampling=8 --thickness=1000 --lowpass_diameter_x=45 --lowpass_diameter_y=45 --lowpass_apod_x=112.5 --lowpass_apod_y=112.5 --highpass_diameter_x=5189 --highpass_diameter_y=5189 --highpass_apod_x=2595 --highpass_apod_y=2595 --corr_mode=mcf --preprocessing=true --border=100 --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false --imod_coarse_align=True --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=214 --mask_width_y=206 --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=1000 --peak_search_radius_y=1000 --logging=true --loglevel=2 --image_file_type=mrc --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true --create_reconstruction=true --show_window_size=true --keep_recons=false --slab=true --map_size_x=479 --map_size_y=463 --video_type=html5vid --defocus_estimate=True --center_all_images=True --re_center_images=True --further_alignment=False --runname=tiltseries0017 --rundir=/gpfs/appion/jbrasch/19feb06g/protomo_alignments/tiltseries0017 --tiltseries=17 --defocus=4.1203128054538 --sessionname=19feb06g --pixelsize=2.7975 --dimx=3838 --dimy=3710 --coarse=True --projectid=282 --expid=8521 --jobtype=protomo

node22
Start time: 2019yr02m08d-10hr45m41s
Description: 
Preparing raw images and initial tilt file
No images were removed from the .tlt file due to high shifts.
Starting Protomo alignment
Creating initial tilt-series video in the background...
Performing IMOD coarse alignment alongside Protomo coarse alignment in the background...
Creating Depiction Videos in Parallel...
Creating Coarse Alignment tilt-series video...
Generating Coarse Alignment reconstruction...
Creating IMOD Coarse Alignment tilt-series video...
Finished Coarse Alignment for Tilt-Series #17!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly post your issue on the following Appion-Protomo Google group or email Alex at anoble@nysbc.org explaining the issue and include this log file.
https://groups.google.com/forum/#!topic/appion-protomo
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2019yr02m08d-10hr57m13s