protomo2aligner.py --negative=-48.8 --positive=46.2 --dose_presets=Moderate --frame_aligned=True --parallel=True --region_x=1919 --region_y=1855 --sampling=8 --map_sampling=8 --thickness=1000 --lowpass_diameter_x=30 --lowpass_diameter_y=30 --lowpass_apod_x=75 --lowpass_apod_y=75 --highpass_diameter_x=3406 --highpass_diameter_y=3406 --highpass_apod_x=1703 --highpass_apod_y=1703 --corr_mode=mcf --preprocessing=true --exclude_images_by_angle_accuracy=0.05 --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=239 --mask_width_y=231 --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 --shift_limit=90 --angle_limit=90 --defocus_estimate=True --defocus_min=3.2 --defocus_max=4.8 --defocus_difference=0.2 --amp_contrast_defocus=0.07 --res_min=10000 --res_max=7.3 --center_all_images=True --re_center_images=True --change_refimg=True --desired_ref_tilt_angle=0 --further_alignment=False --runname=tiltseries0023 --rundir=/gpfs/appion/jbrasch/18nov10g/protomo_alignments/tiltseries0023 --tiltseries=23 --sessionname=18nov10g --pixelsize=1.83586 --dimx=3838 --dimy=3710 --coarse=True --projectid=282 --expid=7953 --jobtype=protomo

node37
Start time: 2018yr12m10d-14hr52m14s
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 #23!
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: 2018yr12m10d-15hr05m35s