MotionCor2 error "No such file or directory"

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

Welcome to the forum @moog.
Thank you for the information you have provided.
Could there be a typo in the cryoSPARC version number that you posted earlier?
Please confirm your cryoSPARC version, including any patches applied, with this command:
cryosparcm status | grep version
Also, what files are listed in (that’s a single line command):
find /data/cryosparc_reult/EMPIAR_10528/P11/J37/motioncor2_logs/ -type f -exec ls -al {} \;

Current cryoSPARC version: v3.3.2

spuser@spgpu:/opt/bin$ find /data/cryosparc_reult/EMPIAR_10528/P11/J37/motioncor2_logs/ -type f -exec ls -al {} ;
spuser@spgpu:/opt/bin$

under motioncor2 folder has no file

The same error with MorCor2 v1.4.7.
v1.4.5 works.

1 Like

menmt thanks for your help it works