Hi,
When I performed MotionCor2 for correction ,
first 1 micrographs are motion corrected well.
But, after this , it showed error message :
[CPU: 98.6 MB] --------------------------------------------------------------
[CPU: 98.6 MB] Processed 0 of 5 movies in 0.01s
[CPU: 98.6 MB] Raw movie filepath located at: J13/imported/015601308562323847588_JP_DJL_Rib_F1037SB_0040.tif - creating MotionCor2 command string...
[CPU: 8.97 GB] Finished creating MotionCor2 command string in 10.35s
[CPU: 8.97 GB] Starting MotionCor2 process...
[CPU: 8.97 GB] Running MotionCor2 command: /home/install/MotionCor2_1.4.7/MotionCor2_1.4.7_Cuda114_12-07-2021 -InTiff /data/cryosparc_reult/EMPIAR_10528/P11/J13/imported/015601308562323847588_JP_DJL_Rib_F1037SB_0040.tif -OutMrc /data/cryosparc_reult/EMPIAR_10528/P11/J37/motioncorrected/015601308562323847588_JP_DJL_Rib_F1037SB_0040_motioncor2_aligned.mrc -Patch 5.0 5.0 -Kv 300.0 -PixSize 0.8261 -FmDose 0.785148545066909 -Gpu 0 1 -GpuMemUsage 0.9 -LogFile /data/cryosparc_reult/EMPIAR_10528/P11/J37/motioncor2_logs/0
[CPU: 8.97 GB] Running process 3659977
[CPU: 8.97 GB] Finished MotionCor2 process in 31.17s
[CPU: 8.97 GB] Traceback (most recent call last):
File "cryosparc_worker/cryosparc_compute/run.py", line 85, in cryosparc_compute.run.main
File "/opt/cryosparc/cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_motioncor2.py", line 397, in run_motioncor2_wrapper
global_shifts = parse_global_alignment(full_frame_log_abs)
File "/opt/cryosparc/cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_motioncor2.py", line 21, in parse_global_alignment
with open(full_frame_alignment_log) as logfile:
FileNotFoundError: [Errno 2] No such file or directory: '/data/cryosparc_reult/EMPIAR_10528/P11/J37/motioncor2_logs/00-Patch-Full.log'
my cryoSPARC is ver 3.2.2
thanks
job log : /home/install/MotionCor2_1.4.7/MotionCor2_1.4.7_Cuda114_12-07-2021: /opt/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/libtiff.so: no version information available (required by /home/install/MotionCor2_1.4.7/MotionCor2_1.4.7_Cuda114_12-07-2021)
-InMrc
-InTiff /data/cryosparc_reult/EMPIAR_10528/P11/J13/imported/015601308562323847588_JP_DJL_Rib_F1037SB_0040.tif
-InEe========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
***************************************************************
Running job on hostname %s spgpu
Allocated Resources : {'fixed': {'SSD': False}, 'hostname': 'spgpu', 'lane': 'default', 'lane_type': 'default', 'license': False, 'licenses_acquired': 0, 'slots': {'CPU': [0, 1], 'GPU': [0, 1], 'RAM': [0, 1]}, 'target': {'cache_path': '/ssd/cryosparc_cache', 'cache_quota_mb': None, 'cache_reserve_mb': 10000, 'desc': None, 'gpus': [{'id': 0, 'mem': 25447170048, 'name': 'NVIDIA GeForce RTX 3090'}, {'id': 1, 'mem': 25445793792, 'name': 'NVIDIA GeForce RTX 3090'}, {'id': 2, 'mem': 25447170048, 'name': 'NVIDIA GeForce RTX 3090'}, {'id': 3, 'mem': 25447170048, 'name': 'NVIDIA GeForce RTX 3090'}], 'hostname': 'spgpu', 'lane': 'default', 'monitor_port': None, 'name': 'spgpu', 'resource_fixed': {'SSD': True}, 'resource_slots': {'CPU': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63], 'GPU': [0, 1, 2, 3], 'RAM': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]}, 'ssh_str': 'spuser@spgpu', 'title': 'Worker node spgpu', 'type': 'node', 'worker_bin_path': '/opt/cryosparc/cryosparc_worker/bin/cryosparcw'}}
**** handle exception rc
set status to failed
========= main process now complete.
========= monitor process now complete.
GB) 0.00 s
GPU 1 Allocation time: GPU ( 1.10 GB) 0.00 s, CPU ( 0.00 GB) 0.00 s
GPU 0 Allocation time: GPU ( 0.04 GB) 0.00 s, CPU ( 0.00 GB) 0.00 s
GPU 1 Allocation time: GPU ( 0.04 GB) 0.00 s, CPU ( 0.00 GB) 0.00 s
GPU 0 Allocation time: GPU ( 14.75 GB) 0.02 s, CPU ( 3.16 GB) 1.46 s
GPU 1 Allocation time: GPU ( 14.75 GB) 0.01 s, CPU ( 2.81 GB) 1.29 s
Create buffers: total memory allocation 8.94 GB
Create buffers: 3.34 seconds
Load Tiff movie: 16.13 seconds
Warning: Gain ref not found.
...... Gain correction will be skipped.
Apply gain: 2.90 seconds
Detect bad and hot pixels.
CC Mean Std: 1.339e-01 9.944e-02
CC threshold: 0.731
Mean & Std: 8.96 3.13
Hot pixel threshold: 27.74
Patch based alignment
Forward FFT of stack, please wait...
Fourier transform done.
Stack for correlation has been generated.
Full-frame alignment has been started.
Iteration 1 Error: 15.422
Iteration 2 Error: 7.892
Iteration 3 Error: 3.252
Iteration 4 Error: 1.274
Iteration 5 Error: 0.493
Full-frame alignment shift
...... Frame ( 1) shift: -24.470 7.990
...... Frame ( 2) shift: -26.000 6.760
...... Frame ( 3) shift: -24.230 6.710
...... Frame ( 4) shift: -20.650 6.470
...... Frame ( 5) shift: -23.010 4.770
...... Frame ( 6) shift: -22.780 2.790
...... Frame ( 7) shift: -22.100 3.850
...... Frame ( 8) shift: -24.370 1.510
...... Frame ( 9) shift: -22.320 1.140
...... Frame ( 10) shift: -24.790 0.180
...... Frame ( 11) shift: -23.330 1.790
...... Frame ( 12) shift: -23.080 3.440
...... Frame ( 13) shift: -20.490 2.800
...... Frame ( 14) shift: -20.120 0.940
...... Frame ( 15) shift: -17.820 0.660
...... Frame ( 16) shift: -18.740 -0.140
...... Frame ( 17) shift: -15.930 -0.480
...... Frame ( 18) shift: -16.410 -0.020
...... Frame ( 19) shift: -14.790 -0.610
...... Frame ( 20) shift: -14.540 0.010
...... Frame ( 21) shift: -15.920 -0.430
...... Frame ( 22) shift: -13.600 0.190
...... Frame ( 23) shift: -13.690 1.900
...... Frame ( 24) shift: -13.130 1.520
...... Frame ( 25) shift: -12.780 1.600
...... Frame ( 26) shift: -13.920 2.710
...... Frame ( 27) shift: -13.530 1.510
...... Frame ( 28) shift: -12.900 0.370
...... Frame ( 29) shift: -11.270 -1.040
...... Frame ( 30) shift: -13.070 -0.130
...... Frame ( 31) shift: -10.720 -1.120
...... Frame ( 32) shift: -11.580 -0.220
...... Frame ( 33) shift: -11.250 -0.870
...... Frame ( 34) shift: -8.020 -2.800
...... Frame ( 35) shift: -8.930 -3.030
...... Frame ( 36) shift: -8.500 -1.840
...... Frame ( 37) shift: -6.850 -1.030
...... Frame ( 38) shift: -6.220 1.480
...... Frame ( 39) shift: -6.180 -0.160
...... Frame ( 40) shift: -6.170 -0.420
...... Frame ( 41) shift: -5.950 0.950
...... Frame ( 42) shift: -5.160 3.100
...... Frame ( 43) shift: -4.680 3.400
...... Frame ( 44) shift: -3.380 1.940
...... Frame ( 45) shift: -1.770 2.520
...... Frame ( 46) shift: -1.130 1.450
...... Frame ( 47) shift: -3.170 1.530
...... Frame ( 48) shift: -1.310 0.750
...... Frame ( 49) shift: -1.000 0.480
...... Frame ( 50) shift: 0.340 1.380
...... Frame ( 51) shift: 0.000 0.000
...... Frame ( 52) shift: -0.640 1.280
...... Frame ( 53) shift: 0.730 -0.070
...... Frame ( 54) shift: 1.130 0.270
...... Frame ( 55) shift: 2.160 -0.140
...... Frame ( 56) shift: 2.760 0.570
...... Frame ( 57) shift: 2.180 0.440
...... Frame ( 58) shift: 3.120 -0.570
...... Frame ( 59) shift: 3.040 0.530
...... Frame ( 60) shift: 1.550 0.600
...... Frame ( 61) shift: 2.400 -0.970
...... Frame ( 62) shift: 1.730 -1.910
...... Frame ( 63) shift: 2.470 -1.040
...... Frame ( 64) shift: 1.600 -0.490
...... Frame ( 65) shift: 0.460 -0.420
...... Frame ( 66) shift: 0.380 -0.110
...... Frame ( 67) shift: 3.150 -0.530
...... Frame ( 68) shift: 3.440 0.610
...... Frame ( 69) shift: 4.320 -0.230
...... Frame ( 70) shift: 3.840 -1.400
...... Frame ( 71) shift: 3.290 -1.090
...... Frame ( 72) shift: 5.130 -1.750
...... Frame ( 73) shift: 4.510 -2.120
...... Frame ( 74) shift: 4.920 0.030
...... Frame ( 75) shift: 5.520 -3.150
...... Frame ( 76) shift: 5.770 -1.800
...... Frame ( 77) shift: 7.240 -2.740
...... Frame ( 78) shift: 7.330 -2.890
...... Frame ( 79) shift: 7.960 -2.910
...... Frame ( 80) shift: 8.630 -3.820
...... Frame ( 81) shift: 8.870 -3.020
...... Frame ( 82) shift: 10.280 -3.930
...... Frame ( 83) shift: 10.130 -3.380
...... Frame ( 84) shift: 8.840 -3.300
...... Frame ( 85) shift: 11.050 -3.900
...... Frame ( 86) shift: 10.990 -3.960
...... Frame ( 87) shift: 13.350 -3.560
...... Frame ( 88) shift: 11.980 -3.020
...... Frame ( 89) shift: 13.540 -4.820
...... Frame ( 90) shift: 13.720 -6.200
...... Frame ( 91) shift: 13.750 -4.190
...... Frame ( 92) shift: 13.640 -4.890
...... Frame ( 93) shift: 12.560 -5.940
...... Frame ( 94) shift: 13.440 -6.390
...... Frame ( 95) shift: 11.980 -6.540
...... Frame ( 96) shift: 12.670 -6.370
...... Frame ( 97) shift: 11.320 -6.560
...... Frame ( 98) shift: 13.920 -6.480
...... Frame ( 99) shift: 13.840 -4.680
...... Frame (100) shift: 14.770 -4.550
...... Frame (101) shift: 12.590 -6.680
Global shifts are corrected: 1.083916 sec
Start to align patches.
Align patch 1 24 left
Iteration 1 Error: 117.157
Iteration 2 Error: 122.947
Iteration 3 Error: 121.821
Iteration 4 Error: 128.002
Iteration 5 Error: 127.137
Iteration 6 Error: 127.298
Iteration 7 Error: 126.987
Align patch 2 23 left
Iteration 1 Error: 82.342
Iteration 2 Error: 81.124
Iteration 3 Error: 83.182
Iteration 4 Error: 82.831
Iteration 5 Error: 124.525
Iteration 6 Error: 110.494
Iteration 7 Error: 108.965
Align patch 3 22 left
Iteration 1 Error: 111.363
Iteration 2 Error: 123.853
Iteration 3 Error: 124.521
Iteration 4 Error: 123.793
Iteration 5 Error: 123.449
Iteration 6 Error: 123.569
Iteration 7 Error: 122.867
Align patch 4 21 left
Iteration 1 Error: 139.292
Iteration 2 Error: 136.436
Iteration 3 Error: 166.657
Iteration 4 Error: 166.258
Iteration 5 Error: 168.778
Iteration 6 Error: 164.126
Iteration 7 Error: 164.414
Align patch 5 20 left
Iteration 1 Error: 158.501
Iteration 2 Error: 159.910
Iteration 3 Error: 163.299
Iteration 4 Error: 164.124
Iteration 5 Error: 164.189
Iteration 6 Error: 164.624
Iteration 7 Error: 164.816
Align patch 6 19 left
Iteration 1 Error: 159.165
Iteration 2 Error: 162.232
Iteration 3 Error: 125.117
Iteration 4 Error: 125.470
Iteration 5 Error: 127.776
Iteration 6 Error: 120.676
Iteration 7 Error: 120.721
Align patch 7 18 left
Iteration 1 Error: 157.255
Iteration 2 Error: 152.407
Iteration 3 Error: 153.786
Iteration 4 Error: 153.069
Iteration 5 Error: 153.187
Iteration 6 Error: 168.844
Iteration 7 Error: 164.032
Align patch 8 17 left
Iteration 1 Error: 165.096
Iteration 2 Error: 149.095
Iteration 3 Error: 137.112
Iteration 4 Error: 135.855
Iteration 5 Error: 135.927
Iteration 6 Error: 135.171
Iteration 7 Error: 137.629
Align patch 9 16 left
Iteration 1 Error: 151.144
Iteration 2 Error: 122.219
Iteration 3 Error: 161.401
Iteration 4 Error: 139.481
Iteration 5 Error: 121.864
Iteration 6 Error: 136.457
Iteration 7 Error: 137.499
Align patch 10 15 left
Iteration 1 Error: 145.085
Iteration 2 Error: 139.977
Iteration 3 Error: 137.393
Iteration 4 Error: 137.436
Iteration 5 Error: 138.346
Iteration 6 Error: 138.462
Iteration 7 Error: 138.469
Align patch 11 14 left
Iteration 1 Error: 153.615
Iteration 2 Error: 169.774
Iteration 3 Error: 168.390
Iteration 4 Error: 131.560
Iteration 5 Error: 131.845
Iteration 6 Error: 132.054
Iteration 7 Error: 156.590
Align patch 12 13 left
Iteration 1 Error: 133.820
Iteration 2 Error: 135.319
Iteration 3 Error: 111.186
Iteration 4 Error: 141.778
Iteration 5 Error: 141.270
Iteration 6 Error: 141.096
Iteration 7 Error: 141.338
Align patch 13 12 left
Iteration 1 Error: 166.620
Iteration 2 Error: 157.273
Iteration 3 Error: 158.712
Iteration 4 Error: 157.547
Iteration 5 Error: 158.327
Iteration 6 Error: 158.403
Iteration 7 Error: 158.982
Align patch 14 11 left
Iteration 1 Error: 109.834
Iteration 2 Error: 147.568
Iteration 3 Error: 147.916
Iteration 4 Error: 126.900
Iteration 5 Error: 126.973
Iteration 6 Error: 126.864
Iteration 7 Error: 137.242
Align patch 15 10 left
Iteration 1 Error: 109.254
Iteration 2 Error: 131.870
Iteration 3 Error: 99.720
Iteration 4 Error: 99.253
Iteration 5 Error: 99.002
Iteration 6 Error: 98.803
Iteration 7 Error: 98.752
Align patch 16 9 left
Iteration 1 Error: 154.407
Iteration 2 Error: 134.113
Iteration 3 Error: 159.423
Iteration 4 Error: 135.704
Iteration 5 Error: 136.782
Iteration 6 Error: 136.865
Iteration 7 Error: 136.891
Align patch 17 8 left
Iteration 1 Error: 141.893
Iteration 2 Error: 142.374
Iteration 3 Error: 143.589
Iteration 4 Error: 144.194
Iteration 5 Error: 143.796
Iteration 6 Error: 143.938
Iteration 7 Error: 143.537
Align patch 18 7 left
Iteration 1 Error: 116.332
Iteration 2 Error: 109.717
Iteration 3 Error: 136.019
Iteration 4 Error: 135.125
Iteration 5 Error: 136.547
Iteration 6 Error: 136.086
Iteration 7 Error: 136.228
Align patch 19 6 left
Iteration 1 Error: 149.378
Iteration 2 Error: 131.910
Iteration 3 Error: 139.862
Iteration 4 Error: 131.921
Iteration 5 Error: 130.949
Iteration 6 Error: 131.369
Iteration 7 Error: 131.065
Align patch 20 5 left
Iteration 1 Error: 169.579
Iteration 2 Error: 168.339
Iteration 3 Error: 167.975
Iteration 4 Error: 167.647
Iteration 5 Error: 168.770
Iteration 6 Error: 168.180
Iteration 7 Error: 168.076
Align patch 21 4 left
Iteration 1 Error: 152.742
Iteration 2 Error: 143.332
Iteration 3 Error: 125.043
Iteration 4 Error: 129.218
Iteration 5 Error: 135.686
Iteration 6 Error: 136.110
Iteration 7 Error: 135.742
Align patch 22 3 left
Iteration 1 Error: 154.277
Iteration 2 Error: 117.332
Iteration 3 Error: 153.914
Iteration 4 Error: 132.321
Iteration 5 Error: 132.545
Iteration 6 Error: 131.702
Iteration 7 Error: 131.163
Align patch 23 2 left
Iteration 1 Error: 137.268
Iteration 2 Error: 167.323
Iteration 3 Error: 143.569
Iteration 4 Error: 143.124
Iteration 5 Error: 142.534
Iteration 6 Error: 164.508
Iteration 7 Error: 164.628
Align patch 24 1 left
Iteration 1 Error: 129.166
Iteration 2 Error: 124.728
Iteration 3 Error: 124.616
Iteration 4 Error: 134.674
Iteration 5 Error: 124.303
Iteration 6 Error: 79.905
Iteration 7 Error: 79.984
Align patch 25 0 left
Iteration 1 Error: 122.688
Iteration 2 Error: 120.533
Iteration 3 Error: 119.263
Iteration 4 Error: 115.858
Iteration 5 Error: 114.849
Iteration 6 Error: 114.985
Iteration 7 Error: 114.392
1 0 1.86 17.05
2 1 2.25 10.74
3 2 1.72 9.20
4 3 3.47 10.05
5 3 2.29 7.50
6 5 2.13 8.12
7 5 1.37 8.19
8 7 2.10 9.12
9 7 0.80 8.42
10 9 1.37 9.07
11 9 1.64 8.11
12 9 1.96 7.66
13 9 1.81 6.15
14 13 2.22 7.47
15 13 1.59 6.77
16 13 1.36 8.45
17 13 1.19 6.54
18 17 1.35 8.59
19 17 3.14 7.94
20 17 1.36 7.56
21 17 1.46 7.16
22 17 1.13 7.96
23 17 1.52 7.46
24 17 1.19 6.69
25 17 1.44 4.94
26 25 1.48 4.80
27 26 0.92 4.42
28 27 0.10 5.56
29 27 0.62 4.00
30 29 0.34 4.49
31 29 0.26 4.02
32 31 1.09 3.43
33 31 0.81 3.81
34 31 0.65 5.98
35 31 0.90 4.05
36 31 0.34 4.54
37 31 0.39 6.33
38 31 0.91 4.14
39 31 0.44 6.35
40 31 0.82 4.50
41 31 0.86 3.93
42 31 0.96 3.90
43 31 0.75 3.72
44 31 0.85 4.10
45 31 0.78 3.86
46 31 0.94 3.30
47 46 1.07 4.39
48 46 1.13 4.13
49 46 0.24 4.29
50 46 1.63 5.09
51 46 0.44 2.97
52 51 0.63 3.21
53 51 1.14 3.13
54 51 0.44 2.73
55 54 1.07 4.47
56 54 0.96 6.35
57 54 1.69 4.94
58 54 0.78 4.22
59 54 0.63 4.45
60 54 0.19 4.92
61 54 0.25 4.16
62 54 0.32 3.26
63 54 1.61 3.85
64 54 2.07 4.20
65 54 2.24 4.39
66 54 0.76 3.83
67 54 1.07 3.83
68 54 0.70 3.41
69 54 0.48 3.65
70 54 1.19 3.81
71 54 0.60 3.45
72 54 0.45 5.07
73 54 1.76 3.54
74 54 0.67 4.15
75 54 0.86 4.98
76 54 0.76 4.56
77 54 0.71 4.79
78 54 1.53 4.34
79 54 0.99 3.30
80 54 1.63 4.65
81 54 0.71 4.21
82 54 0.47 5.99
83 54 0.63 6.18
84 54 0.14 4.61
85 54 1.48 5.05
86 54 0.67 4.12
87 54 1.06 5.61
88 54 0.57 4.52
89 54 0.62 5.14
90 54 0.30 5.97
91 54 2.13 5.79
92 54 0.71 5.21
93 54 0.31 7.15
94 54 0.93 5.22
95 54 2.01 8.73
96 54 2.94 8.37
97 54 2.41 9.04
98 54 1.30 9.92
99 54 2.36 12.50
100 54 2.50 12.04
Patch alignment time: 0.89(sec)
Mag stretch: 1.000 -0.000
Correction of local motion: 3.409666 sec
Computation time: 11.559918 sec
Saving motion corrected images ......
Saving motion corrected images done.
Save image sums: 1.73 sec
Total time: 29.423035 sec