Reference based motion correction error - could not open file

Motion Correction
1

When running RBMC, I get the following error. (v 4.4.1)

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 95, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_reference_motion.py”, line 322, in cryosparc_master.cryosparc_compute.jobs.motioncorrection.run_reference_motion.run_reference_motion_correction
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/refmotion.py”, line 766, in cryosparc_master.cryosparc_compute.jobs.motioncorrection.refmotion.mainfn_param_optimize
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/refmotion.py”, line 674, in cryosparc_master.cryosparc_compute.jobs.motioncorrection.refmotion.prepare_datasets
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/refmotion.py”, line 143, in cryosparc_master.cryosparc_compute.jobs.motioncorrection.refmotion.read_gain_and_defects
File “cryosparc_master/cryosparc_compute/blobio/prefetch.py”, line 70, in cryosparc_master.cryosparc_compute.blobio.prefetch.synchronous_native_read
OSError:

IO request details:
Error ocurred (No such file or directory) at line 667 in fopen

Could not open file. Make sure the path exists.

filename: /mnt/4extra_hdd/RM240425_12_24/2967/CS-skik/J1/imported/CountCDSRef_SKIK_51_000.mrc
filetype: 0
header_only: 0
idx_start: 0
idx_limit: -1
eer_upsampfactor: 2
eer_numfractions: 40
num_threads: 6
buffer: (nil)
buffer_sz: 0
nx, ny, nz: 0 0 0
dtype: 0
total_time: -1.000000
io_time: 0.000000

2

Imported movie files are represented by symbolic links inside the CryoSPARC project directory. The targets of these links (the actual movie files) need to be available for reference-based motion correction.
What are the outputs of these commands:

ls -l /mnt/4extra_hdd/RM240425_12_24/2967/CS-skik/J1/imported/CountCDSRef_SKIK_51_000.mrc
readlink -e /mnt/4extra_hdd/RM240425_12_24/2967/CS-skik/J1/imported/CountCDSRef_SKIK_51_000.mrc
3

@wtempel
Thank you for replying !
The outputs are as follows.

[root@AOBA ~]# ls -l /mnt/4extra_hdd/RM240425_12_24/2967/CS-skik/J1/imported/CountCDSRef_SKIK_51_000.mrc
lrwxrwxrwx 1 cryosparc cryosparc 74 5月 13 16:47 /mnt/4extra_hdd/RM240425_12_24/2967/CS-skik/J1/imported/CountCDSRef_SKIK_51_000.mrc → /mnt/extra_hdd/RM240425_12_24/2967/Micrographs/CountCDSRef_SKIK_51_000.mrc
[root@AOBA ~]# readlink -e /mnt/4extra_hdd/RM240425_12_24/2967/CS-skik/J1/imported/CountCDSRef_SKIK_51_000.mrc
[root@AOBA ~]#

4

Is the file to which the link points:

/mnt/extra_hdd/RM240425_12_24/2967/Micrographs/CountCDSRef_SKIK_51_000.mrc

missing?

5

@wtempel
Yes.
It is in 4extra hdd

Perhaps it has something to do with the fact that we changed calculators from another calculator last week.
I had mounted on extra hdd until last week, unmounted last week, mounted on 4 extra hdd on my current calculator, and attached the previous jobs in cryosparc.

[root@AOBA mnt]# cd extra_hdd/
[root@AOBA extra_hdd]# ls
3075 YT230517_1_4_retry

[root@AOBA mnt]# ls
2extra_hdd 3extra_hdd 4extra_hdd 5extra_hdd 6extra_hdd 7extra_hdd extra_hdd
[root@AOBA mnt]# cd 4extra_hdd/
[root@AOBA 4extra_hdd]# ls
EK231109_2_1 RM240425_12_24
[root@AOBA 4extra_hdd]# cd RM240425_12_24/
[root@AOBA RM240425_12_24]# ls
2964 2965 2966 2967 Reference

6

@wtempel

What should I do ?

7

It seems the symbolic links inside the

/mnt/4extra_hdd/RM240425_12_24/2967/CS-skik/J1/

directory are no longer valid.

You may generally want to minimize the use of the root account to occasions when root access is absolutely required. Many CryoSPARC maintenance task should be performed under the non-privileged Linux account that runs the CryoSPARC service processes.
Please see this guide section on updating symbolic links for imported data.
Alternatively, you may check whether you can simulate the presence of raw data at their original path by placing a symbolic link

cd /mnt/extra_hdd/
ln -s /mnt/4extra_hdd/RM240425_12_24

Caution: The latter method may be easier to implement, but the additional link may confuse you later, or may not resolve the problem.

1 Like