Start time: 2017yr09m04d-10hr05m33s 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=30.0 --r1_peak_search_radius_y=100.0 --r1_peak_search_radius_x=100.0 --r8_lowpass_apod_y=0.05595 --r8_lowpass_apod_x=0.05595 --all_recon_videos=true --r7_lowpass_diameter_y=0.1119 --r7_lowpass_diameter_x=0.1119 --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=40.0 --r7_iters=0 --r4_lowpass_apod_y=0.1119 --r4_lowpass_apod_x=0.1119 --r6_region_y=512 --r6_region_x=512 --auto_ctf_correct=False --r4_lp=20.0 --r3_lowpass_apod_x=0.2238 --r3_lowpass_apod_y=0.2238 --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=0.008952 --r6_peak_search_radius_x=100.0 --reconstruct=False --rotation=true --r2_highpass_apod_y=0.006714 --r5_mask_width_y=1024 --firststep=1 --procs=all --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=0.002238 --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=0.004476 --highpass_diameter_x=0.004476 --r7_highpass_apod_y=0.002238 --r7_highpass_apod_x=0.002238 --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r6_kernel_y=3 --r7_lp=20.0 --r4_lowpass_diameter_y=0.1119 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --r6_mask_apod_y=10 --r1_highpass_diameter_x=0.004476 --lp=20.0 --r5_lp=20.0 --r1_highpass_diameter_y=0.004476 --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/anoble/17aug18i/protomo_alignments --r7_mask_apod_y=10 --r3_highpass_diameter_x=0.002238 --r6_body=0 --r7_corr_mode=mcf --auto_reconstruct=False --thickness=2680.96514745 --r5_peak_search_radius_y=100.0 --r1_lowpass_apod_x=0.4476 --r3_mask_apod_x=10 --r2_sampling=6 --recon_lp_diam_y=15 --r3_highpass_apod_x=0.004476 --r6_corr_mode=mcf --r6_kernel_x=3 --runname=tiltseries0007 --r6_highpass_diameter_y=0.002238 --r2_lowpass_diameter_x=0.3357 --r2_lowpass_diameter_y=0.3357 --r6_lp=20.0 --r8_lp=20.0 --r4_highpass_diameter_x=0.001119 --r5_lowpass_diameter_y=0.05595 --r5_lowpass_diameter_x=0.05595 --r8_mask_width_x=1024 --r8_mask_width_y=1024 --link_recons= --show_window_size=true --amp_contrast_ctf=0.07 --r8_lowpass_diameter_x=0.05595 --r8_lowpass_diameter_y=0.05595 --r8_body=0 --r6_lowpass_apod_y=0.2238 --r6_lowpass_apod_x=0.2238 --r4_mask_width_x=1024 --r4_mask_width_y=1024 --r5_highpass_apod_y=0.001119 --auto_convergence=0.015 --mask_apod_y=10 --r7_region_x=512 --r7_lowpass_apod_x=0.1119 --r7_lowpass_apod_y=0.1119 --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=Moderate --r3_lp=20.0 --mask_apod_x=10 --r3_peak_search_radius_x=100.0 --r5_highpass_diameter_x=0.0005595 --highpass_apod_y=0.008952 --defocus_estimate=False --r4_iters=0 --dose_a=0.245 --refresh_i3t=False --r1_highpass_apod_y=0.008952 --r1_highpass_apod_x=0.008952 --r2_highpass_apod_x=0.006714 --sampling=8 --expid=4732 --r5_lowpass_apod_x=0.05595 --r5_lowpass_apod_y=0.05595 --auto_convergence_iters=5 --r1_lowpass_diameter_y=0.4476 --r1_lowpass_diameter_x=0.4476 --r4_sampling=2 --res_max=10 --r4_lowpass_diameter_x=0.1119 --fix_images=False --r6_highpass_diameter_x=0.002238 --r7_region_y=512 --dose_b=-1.665 --positive=90.0 --r3_peak_search_radius_y=100.0 --r7_highpass_diameter_x=0.001119 --negative=-90.0 --r2_peak_search_radius_y=100.0 --r8_kernel_y=3 --tiltseriesranges=7-63 --r5_corr_mode=mcf --change_refimg=True --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=0.001119 --r6_sampling=4 --mask_width_x=1024 --r7_highpass_diameter_y=0.001119 --r1_lowpass_apod_y=0.4476 --r6_mask_apod_x=10 --r5_sampling=1 --coarse_param_file=/gpfs/appion/anoble/17aug18i/protomo_alignments//tiltseries0005/coarse_series0005.param --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=0.003357 --prep_files=True --sessionname=17aug18i --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=0.001119 --r1_iters=1 --r5_highpass_diameter_y=0.0005595 --recon_thickness=2000.0 --defocus_max=0 --r4_region_y=512 --r3_highpass_apod_y=0.004476 --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=0.0005595 --r3_lowpass_diameter_x=0.2238 --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=304 --r6_mask_width_x=1024 --r6_mask_width_y=1024 --r8_iters=0 --iter_gradient=true --r3_body=0 --r3_lowpass_diameter_y=0.2238 --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=0.5595 --r2_highpass_diameter_x=0.003357 --map_size_z=375 --lowpass_diameter_x=0.4476 --lowpass_diameter_y=0.4476 --r8_mask_apod_y=10 --r8_mask_apod_x=10 --r6_highpass_apod_x=0.004476 --r6_highpass_apod_y=0.004476 --r3_corr_mode=mcf --r2_lowpass_apod_y=0.3357 --r3_mask_apod_y=10 --r2_lowpass_apod_x=0.3357 --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=0.001119 --r8_highpass_apod_y=0.001119 --scale=false --video_type=html5vid --auto_prep=False --dimx=7676 --dimy=7420 --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 --r5_kernel_y=3 --lowpass_apod_y=0.4476 --lowpass_apod_x=0.4476 --kernel_x=3 --kernel_y=3 --gradient=true --tilt_clip=true --r4_highpass_apod_x=0.002238 --r4_highpass_apod_y=0.002238 --r6_lowpass_diameter_x=0.2238 --r6_lowpass_diameter_y=0.2238 --r1_mask_width_y=1024 --r1_mask_width_x=1024 --laststep=2 --jobtype=protomo --r8_highpass_diameter_x=0.0005595 Preparing Files and Directories for Protomo 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. 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 #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 #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 #14 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 #14. Preparing Tilt-Series #15 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 #15. Preparing Tilt-Series #16 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 #16. Preparing Tilt-Series #13 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 #13. Preparing Tilt-Series #12 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 #12. Preparing Tilt-Series #17 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 #17. Preparing Tilt-Series #18 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 #18. Preparing Tilt-Series #21 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 #21. Preparing Tilt-Series #20 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 #20. Preparing Tilt-Series #19 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 #19. Preparing Tilt-Series #26 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 #26. Preparing Tilt-Series #22 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 #22. Preparing Tilt-Series #25 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 #25. Preparing Tilt-Series #23 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 #23. Preparing Tilt-Series #24 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 #24. Preparing Tilt-Series #30 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 #30. Preparing Tilt-Series #27 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 #27. Preparing Tilt-Series #28 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 #28. Preparing Tilt-Series #31 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 #31. Preparing Tilt-Series #29 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 #29. Preparing Tilt-Series #34 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 #34. Preparing Tilt-Series #32 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 #32. Preparing Tilt-Series #33 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 #33. Preparing Tilt-Series #35 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 #35. Preparing Tilt-Series #36 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 #36. Preparing Tilt-Series #41 Images and .tlt File... Creating initial tilt-series video... Images [1, 2] were removed from the tilt file because their shifts exceed 30.0% of the (x) and/or (y) dimensions. Images [3, 4, 5, 6, 7, 8, 9, 10, 11, 12] exceeded the allowed shift, but were at tilt angles less than the 40.0 degree angle limit. Finished Preparing Files and Directories for Tilt-Series #41. Preparing Tilt-Series #37 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 #37. Preparing Tilt-Series #38 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 #38. Preparing Tilt-Series #40 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 #40. Preparing Tilt-Series #39 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 #39. Preparing Tilt-Series #42 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 #42. Preparing Tilt-Series #43 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 #43. Preparing Tilt-Series #45 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 #45. Preparing Tilt-Series #46 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 #46. Preparing Tilt-Series #44 Images and .tlt File... Creating initial tilt-series video... Images [1, 2] were removed from the tilt file because their shifts exceed 30.0% of the (x) and/or (y) dimensions. Images [3, 4, 5, 6, 7, 8, 9, 10, 11, 12] exceeded the allowed shift, but were at tilt angles less than the 40.0 degree angle limit. Finished Preparing Files and Directories for Tilt-Series #44. Preparing Tilt-Series #50 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 #50. Preparing Tilt-Series #47 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 #47. Preparing Tilt-Series #48 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 #48. Preparing Tilt-Series #49 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 #49. Preparing Tilt-Series #51 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 #51. Preparing Tilt-Series #54 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 #54. Preparing Tilt-Series #53 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 #53. Preparing Tilt-Series #56 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 #56. Preparing Tilt-Series #52 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 #52. Preparing Tilt-Series #55 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 #55. Preparing Tilt-Series #59 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 #59. Preparing Tilt-Series #58 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 #58. Preparing Tilt-Series #57 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 #57. Preparing Tilt-Series #60 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 #60. Preparing Tilt-Series #61 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 #61. Preparing Tilt-Series #63 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 #63. Preparing Tilt-Series #62 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 #62. Performing Dose Compensation Dose Compensation Finished for Tilt-Series 7-63! Files and Directories Prepared for Tilt-Series 7-63!Performing Coarse Alignments Coarse Alignments Finished for Tilt-Series 7-63! Did everything blow up and now you're yelling at your computer screen? If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file. 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: 2017yr09m04d-12hr25m04s