Start time: 2019yr05m13d-11hr41m21s Description: protomo2batch.py --auto_refine=False --r2_mask_apod_y=10 --r5_kernel_x=3 --recon_lowpass=False --amp_contrast_defocus=0.07 --r3_kernel_x=3 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --r8_corr_mode=mcf --r7_mask_apod_x=10 --shift_limit=90.0 --r1_peak_search_radius_y=100.0 --r1_peak_search_radius_x=100.0 --r8_lowpass_apod_y=0.183586 --r8_lowpass_apod_x=0.183586 --all_recon_videos=true --r7_lowpass_diameter_y=0.367172 --r7_lowpass_diameter_x=0.367172 --r4_corr_mode=mcf --r1_region_x=512 --r1_region_y=512 --r5_mask_width_x=1024 --r2_corr_mode=mcf --recon_lp_diam_x=15 --angle_limit=90.0 --r7_iters=0 --r4_lowpass_apod_y=0.367172 --r4_lowpass_apod_x=0.367172 --r6_region_y=512 --r6_region_x=512 --auto_ctf_correct=False --r4_lp=20.0 --r3_lowpass_apod_x=0.734344 --r3_lowpass_apod_y=0.734344 --screening_mode=False --r5_body=0 --r2_region_y=512 --r2_region_x=512 --r8_region_y=512 --r8_region_x=512 --screening_start=1 --r7_kernel_y=3 --r7_kernel_x=3 --highpass_apod_x=0.02937376 --r6_peak_search_radius_x=100.0 --reconstruct=False --rotation=true --r2_highpass_apod_y=0.02203032 --r5_mask_width_y=1024 --firststep=1 --procs=all --frame_aligned=True --image_file_type=mrc --imod_coarse_align=True --r2_sampling=6 --r2_mask_width_x=1024 --r2_mask_width_y=1024 --r2_lp=20.0 --r4_region_x=512 --r5_region_x=512 --r5_region_y=512 --highpass_diameter_y=0.01468688 --highpass_diameter_x=0.01468688 --r7_highpass_apod_y=0.00734344 --r7_highpass_apod_x=0.00734344 --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r6_kernel_y=3 --r7_lp=20.0 --r4_lowpass_diameter_y=0.367172 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --r6_mask_apod_y=10 --r1_highpass_diameter_x=0.01468688 --lp=20.0 --r5_lp=20.0 --r1_highpass_diameter_y=0.01468688 --r4_kernel_x=3 --r4_kernel_y=3 --r7_body=0 --peak_search_radius_x=100.0 --peak_search_radius_y=100.0 --rundir=/gpfs/appion/jbrasch/19mar29h/protomo_alignments --r7_mask_apod_y=10 --r3_highpass_diameter_x=0.00734344 --r6_body=0 --r7_corr_mode=mcf --auto_reconstruct=False --thickness=817.05576678 --r5_peak_search_radius_y=100.0 --r1_lowpass_apod_x=1.468688 --r3_mask_apod_x=10 --exporting=False --recon_lp_diam_y=15 --r3_highpass_apod_x=0.01468688 --r6_corr_mode=mcf --r6_kernel_x=3 --runname=tiltseries0002 --r6_highpass_diameter_y=0.00734344 --r2_lowpass_diameter_x=1.101516 --r2_lowpass_diameter_y=1.101516 --r6_lp=20.0 --r8_lp=20.0 --r4_highpass_diameter_x=0.00367172 --r5_lowpass_diameter_y=0.183586 --r5_lowpass_diameter_x=0.183586 --r8_mask_width_x=1024 --r8_mask_width_y=1024 --link_recons= --center_all_images=False --show_window_size=true --amp_contrast_ctf=0.07 --r8_lowpass_diameter_x=0.183586 --r8_lowpass_diameter_y=0.183586 --r8_body=0 --r6_lowpass_apod_y=0.734344 --r6_lowpass_apod_x=0.734344 --change_refimg=True --r4_mask_width_y=1024 --r5_highpass_apod_y=0.00367172 --auto_convergence=0.015 --mask_apod_y=10 --r7_region_x=512 --r7_lowpass_apod_x=0.367172 --r7_lowpass_apod_y=0.367172 --defocus_tlt_iteration=0 --DefocusTol=200 --all_tilt_videos=true --r6_iters=0 --r7_sampling=2 --iWidth=20 --r1_kernel_y=3 --r1_kernel_x=3 --dose_presets=False --r3_lp=20.0 --mask_apod_x=10 --r3_peak_search_radius_x=100.0 --r5_highpass_diameter_x=0.00183586 --highpass_apod_y=0.02937376 --defocus_estimate=False --r4_iters=0 --dose_a=0.245 --refresh_i3t=False --r1_highpass_apod_y=0.02937376 --r1_highpass_apod_x=0.02937376 --r2_highpass_apod_x=0.02203032 --sampling=8 --expid=8799 --r5_lowpass_apod_x=0.183586 --r5_lowpass_apod_y=0.183586 --auto_convergence_iters=5 --r1_lowpass_diameter_y=1.468688 --r1_lowpass_diameter_x=1.468688 --r4_sampling=2 --res_max=10 --r4_lowpass_diameter_x=0.367172 --fix_images=False --r6_highpass_diameter_x=0.00734344 --r7_region_y=512 --dose_b=-1.665 --positive=90.0 --r3_peak_search_radius_y=100.0 --r7_highpass_diameter_x=0.00367172 --negative=-90.0 --r2_peak_search_radius_y=100.0 --r8_kernel_y=3 --tiltseriesranges=2-11 --r5_corr_mode=mcf --r4_mask_width_x=1024 --r3_mask_width_y=1024 --r3_mask_width_x=1024 --map_sampling=8 --dose_c=2.81 --recon_map_sampling=2 --res_min=10000 --r2_iters=0 --coarse_align=True --r4_highpass_diameter_y=0.00367172 --r6_sampling=4 --mask_width_x=1024 --r7_highpass_diameter_y=0.00367172 --r1_lowpass_apod_y=1.468688 --r6_mask_apod_x=10 --r5_sampling=1 --coarse_param_file=/gpfs/appion/jbrasch/19mar29h/protomo_alignments//tiltseries0001/coarse_series0001.param --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=0.01101516 --prep_files=True --sessionname=19mar29h --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=0.00367172 --r1_iters=1 --r5_highpass_diameter_y=0.00183586 --recon_thickness=2000.0 --defocus_max=0 --r4_region_y=512 --r3_highpass_apod_y=0.01468688 --r3_kernel_y=3 --recon_map_size_y=2048 --recon_map_size_x=2048 --r3_region_x=512 --r3_region_y=512 --r4_body=0 --r3_iters=0 --r2_peak_search_radius_x=100.0 --r8_sampling=1 --r7_mask_width_y=1024 --r7_mask_width_x=1024 --r8_highpass_diameter_y=0.00183586 --r3_lowpass_diameter_x=0.734344 --r1_mask_apod_y=10 --defocus_tlt=best_bin1or2 --r1_lp=20.0 --auto_scaling=True --r2_body=0 --orientation=true --r7_peak_search_radius_y=100.0 --r7_peak_search_radius_x=100.0 --r8_kernel_x=3 --projectid=282 --r6_mask_width_x=1024 --r6_mask_width_y=1024 --r8_iters=0 --iter_gradient=true --r3_body=0 --r3_lowpass_diameter_y=0.734344 --refine=False --mask_width_y=1024 --azimuth=true --r6_peak_search_radius_y=100.0 --elevation=false --r2_kernel_x=3 --r2_kernel_y=3 --pixelsize=1.83586 --r2_highpass_diameter_x=0.01101516 --map_size_z=375 --lowpass_diameter_x=1.468688 --lowpass_diameter_y=1.468688 --r8_mask_apod_y=10 --r8_mask_apod_x=10 --r6_highpass_apod_x=0.01468688 --r6_highpass_apod_y=0.01468688 --r3_corr_mode=mcf --r2_lowpass_apod_y=1.101516 --r3_mask_apod_y=10 --r2_lowpass_apod_x=1.101516 --auto_coarse_align=False --r3_sampling=4 --description= --r1_corr_mode=mcf --iters=1 --r5_peak_search_radius_x=100.0 --r8_peak_search_radius_x=100.0 --r8_peak_search_radius_y=100.0 --automation=False --r8_highpass_apod_x=0.00367172 --r8_highpass_apod_y=0.00367172 --scale=false --video_type=html5vid --auto_prep=False --dimx=3838 --dimy=3710 --parallel=False --r4_peak_search_radius_x=100.0 --r4_peak_search_radius_y=100.0 --region_y=512 --region_x=512 --auto_elevation=True --r3_highpass_diameter_y=0.00734344 --r5_kernel_y=3 --lowpass_apod_y=1.468688 --lowpass_apod_x=1.468688 --kernel_x=3 --kernel_y=3 --gradient=true --tilt_clip=true --r4_highpass_apod_x=0.00734344 --r4_highpass_apod_y=0.00734344 --r6_lowpass_diameter_x=0.734344 --r6_lowpass_diameter_y=0.734344 --r1_mask_width_y=1024 --r1_mask_width_x=1024 --laststep=2 --jobtype=protomo --r8_highpass_diameter_x=0.00183586 Preparing Files and Directories for Protomo Preparing Tilt-Series #6 Images and .tlt File... Creating initial tilt-series video... No images were removed from the .tlt file due to high shifts. Finished Preparing Files and Directories for Tilt-Series #6. Preparing Tilt-Series #3 Images and .tlt File... Creating initial tilt-series video... No images were removed from the .tlt file due to high shifts. Finished Preparing Files and Directories for Tilt-Series #3. Preparing Tilt-Series #5 Images and .tlt File... Creating initial tilt-series video... No images were removed from the .tlt file due to high shifts. Finished Preparing Files and Directories for Tilt-Series #5. Preparing Tilt-Series #4 Images and .tlt File... Creating initial tilt-series video... No images were removed from the .tlt file due to high shifts. Finished Preparing Files and Directories for Tilt-Series #4. Preparing Tilt-Series #7 Images and .tlt File... Creating initial tilt-series video... No images were removed from the .tlt file due to high shifts. Finished Preparing Files and Directories for Tilt-Series #7. Preparing Tilt-Series #9 Images and .tlt File... Creating initial tilt-series video... No images were removed from the .tlt file due to high shifts. Finished Preparing Files and Directories for Tilt-Series #9. Preparing Tilt-Series #2 Images and .tlt File... Creating initial tilt-series video... No images were removed from the .tlt file due to high shifts. Finished Preparing Files and Directories for Tilt-Series #2. Preparing Tilt-Series #8 Images and .tlt File... Creating initial tilt-series video... No images were removed from the .tlt file due to high shifts. Finished Preparing Files and Directories for Tilt-Series #8. Preparing Tilt-Series #10 Images and .tlt File... Creating initial tilt-series video... No images were removed from the .tlt file due to high shifts. Finished Preparing Files and Directories for Tilt-Series #10. Preparing Tilt-Series #11 Images and .tlt File... Creating initial tilt-series video... No images were removed from the .tlt file due to high shifts. Finished Preparing Files and Directories for Tilt-Series #11. Files and Directories Prepared for Tilt-Series 2-11!Performing Protomo Coarse Alignments Starting Protomo Coarse Alignment for Tilt-Series #10 Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #1 with Window Size: (224, 224) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #2 with Window Size: (216, 216) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #3 with Window Size: (210, 210) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #4 with Window Size: (200, 200) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #5 with Window Size: (196, 196) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #6 with Window Size: (192, 192) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #7 with Window Size: (180, 180) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #8 with Window Size: (168, 168) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #9 with Window Size: (162, 162) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #10 with Window Size: (160, 160) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #11 with Window Size: (150, 150) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #12 with Window Size: (144, 144) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #13 with Window Size: (140, 140) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #10 failed. Retry #14 with Window Size: (128, 128) (at sampling 8)... Creating Protomo Coarse Alignment Depiction Videos Creating Protomo Coarse Alignment tilt-series video... Generating Protomo Coarse Alignment reconstruction... Protomo Coarse Alignment finished for Tilt-Series #10! Starting Protomo Coarse Alignment for Tilt-Series #6 Creating Protomo Coarse Alignment Depiction Videos Creating Protomo Coarse Alignment tilt-series video... Generating Protomo Coarse Alignment reconstruction... Protomo Coarse Alignment finished for Tilt-Series #6! Starting Protomo Coarse Alignment for Tilt-Series #7 Protomo Coarse Alignment for Tilt-Series #7 failed. Retry #1 with Window Size: (224, 224) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #7 failed. Retry #2 with Window Size: (216, 216) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #7 failed. Retry #3 with Window Size: (210, 210) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #7 failed. Retry #4 with Window Size: (200, 200) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #7 failed. Retry #5 with Window Size: (196, 196) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #7 failed. Retry #6 with Window Size: (192, 192) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #7 failed. Retry #7 with Window Size: (180, 180) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #7 failed. Retry #8 with Window Size: (168, 168) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #7 failed. Retry #9 with Window Size: (162, 162) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #7 failed. Retry #10 with Window Size: (160, 160) (at sampling 8)... Protomo Coarse Alignment for Tilt-Series #7 failed. Retry #11 with Window Size: (150, 150) (at sampling 8)... Creating Protomo Coarse Alignment Depiction Videos Creating Protomo Coarse Alignment tilt-series video... Generating Protomo Coarse Alignment reconstruction... Protomo Coarse Alignment finished for Tilt-Series #7! Starting Protomo Coarse Alignment for Tilt-Series #3 Creating Protomo Coarse Alignment Depiction Videos Creating Protomo Coarse Alignment tilt-series video... Generating Protomo Coarse Alignment reconstruction... Protomo Coarse Alignment finished for Tilt-Series #3! Starting Protomo Coarse Alignment for Tilt-Series #11 Creating Protomo Coarse Alignment Depiction Videos Creating Protomo Coarse Alignment tilt-series video... Generating Protomo Coarse Alignment reconstruction... Protomo Coarse Alignment finished for Tilt-Series #11! Starting Protomo Coarse Alignment for Tilt-Series #8 Creating Protomo Coarse Alignment Depiction Videos Creating Protomo Coarse Alignment tilt-series video... Generating Protomo Coarse Alignment reconstruction... Protomo Coarse Alignment finished for Tilt-Series #8! Starting Protomo Coarse Alignment for Tilt-Series #2 Creating Protomo Coarse Alignment Depiction Videos Creating Protomo Coarse Alignment tilt-series video... Generating Protomo Coarse Alignment reconstruction... Protomo Coarse Alignment finished for Tilt-Series #2! Starting Protomo Coarse Alignment for Tilt-Series #5 Creating Protomo Coarse Alignment Depiction Videos Creating Protomo Coarse Alignment tilt-series video... Generating Protomo Coarse Alignment reconstruction... Protomo Coarse Alignment finished for Tilt-Series #5! Starting Protomo Coarse Alignment for Tilt-Series #9 Creating Protomo Coarse Alignment Depiction Videos Creating Protomo Coarse Alignment tilt-series video... Generating Protomo Coarse Alignment reconstruction... Protomo Coarse Alignment finished for Tilt-Series #9! Starting Protomo Coarse Alignment for Tilt-Series #4 Creating Protomo Coarse Alignment Depiction Videos Creating Protomo Coarse Alignment tilt-series video... Generating Protomo Coarse Alignment reconstruction... Protomo Coarse Alignment finished for Tilt-Series #4! Protomo Coarse Alignments Finished for Tilt-Series 2-11! Performing Imod Coarse Alignments Starting Imod Coarse Alignment for Tilt-Series #3 Creating Imod Coarse Alignment tilt-series video Imod Coarse Alignment finished for Tilt-Series #3! Starting Imod Coarse Alignment for Tilt-Series #9 Creating Imod Coarse Alignment tilt-series video Imod Coarse Alignment finished for Tilt-Series #9! Starting Imod Coarse Alignment for Tilt-Series #6 Creating Imod Coarse Alignment tilt-series video Imod Coarse Alignment finished for Tilt-Series #6! Starting Imod Coarse Alignment for Tilt-Series #2 Creating Imod Coarse Alignment tilt-series video Imod Coarse Alignment finished for Tilt-Series #2! Starting Imod Coarse Alignment for Tilt-Series #10 Creating Imod Coarse Alignment tilt-series video Imod Coarse Alignment finished for Tilt-Series #10! Starting Imod Coarse Alignment for Tilt-Series #5 Creating Imod Coarse Alignment tilt-series video Imod Coarse Alignment finished for Tilt-Series #5! Starting Imod Coarse Alignment for Tilt-Series #8 Creating Imod Coarse Alignment tilt-series video Imod Coarse Alignment finished for Tilt-Series #8! Starting Imod Coarse Alignment for Tilt-Series #7 Creating Imod Coarse Alignment tilt-series video Imod Coarse Alignment finished for Tilt-Series #7! Starting Imod Coarse Alignment for Tilt-Series #11 Creating Imod Coarse Alignment tilt-series video Imod Coarse Alignment finished for Tilt-Series #11! Starting Imod Coarse Alignment for Tilt-Series #4 Creating Imod Coarse Alignment tilt-series video Imod Coarse Alignment finished for Tilt-Series #4! Imod Coarse Alignments Finished for Tilt-Series 2-11! 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: 2019yr05m13d-12hr19m32s