protomo2aligner.py --dose_presets=Moderate --frame_aligned=True --parallel=True --region_x=1855 --region_y=1919 --sampling=8 --map_sampling=8 --thickness=500 --lowpass_diameter_x=50 --lowpass_diameter_y=50 --lowpass_apod_x=125 --lowpass_apod_y=125 --highpass_diameter_x=3270 --highpass_diameter_y=3270 --highpass_apod_x=1635 --highpass_apod_y=1635 --corr_mode=mcf --preprocessing=true --border=100 --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false --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=206 --mask_width_y=214 --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=463 --map_size_y=479 --video_type=html5vid --shift_limit=30 --angle_limit=40 --defocus_estimate=True --further_alignment=None --runname=tiltseries0008 --rundir=/gpfs/appion/vdandey/17mar18a/protomo_alignments/tiltseries0008 --tiltseries=8 --defocus=5 --sessionname=17mar18a --pixelsize=1.76302 --dimx=3710 --dimy=3838 --coarse=True --projectid=1 --expid=3662 --jobtype=protomo

node03
Start time: 2017yr03m20d-17hr18m17s
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...
Creating Depiction Videos in Parallel...
Creating Coarse Alignment tilt-series video...
Generating Coarse Alignment reconstruction...
Finished Coarse Alignment for Tilt-Series #8!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org and include this log file.
If everything worked beautifully and you publish it, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr03m20d-17hr26m30s