ValueError: total size of new array must be unchanged - Full Frame Motion Correction

Motion Correction
1

Hi,

Would someone help me with this?
When I start to do motion correction with a data sets form EMPIAR, I got error like this:

Project P10 Job J15 Started
Master running v2.5.0, worker running v2.5.0
Running on lane dcc
Resources allocated:
Worker: dcc
CPU : [0, 1, 2, 3, 4, 5]
GPU : [0]
RAM : [0, 1]
SSD : False
--------------------------------------------------------------
Importing job module for job type rigid_motion_correction...
Job ready to run
***************************************************************
--------------------------------------------------------------

Processed 0 of 1521 movies in 0.01s

Loading raw movie data from J4/imported/BetaGal_20141212_0004_movie.mrcs ...

Done in 39.75s

Processing ...

Done in 16.40s

Writing result to J15/motioncorrected/BetaGal_20141212_0004_movie_rigid_aligned.mrc ...

image

Done in 1.63s


Loading raw movie data from J4/imported/BetaGal_20141212_0006_movie.mrcs ...

Traceback (most recent call last): File "cryosparc2_worker/cryosparc2_compute/run.py", line 78, in cryosparc2_compute.run.main File "cryosparc2_worker/cryosparc2_compute/jobs/motioncorrection/run.py", line 354, in cryosparc2_compute.jobs.motioncorrection.run.run_rigid_motion_correction File "cryosparc2_compute/blobio/mrc.py", line 113, in read_mrc data = read_mrc_data(file_obj, header, start_page, end_page, out) File "cryosparc2_compute/blobio/mrc.py", line 77, in read_mrc_data data = n.fromfile(file_obj, dtype=dtype, count= num_pages * ny * nx) . reshape (num_pages, ny, nx) ValueError: total size of new array must be unchanged
2

This error happens when there is one movie file (in this case J4/imported/BetaGal_20141212_0006_movie.mrcs) that has become corrupt/shortened. The error is saying that the number of bytes in the file is not enough given the size reported by the file header.

3

Thank you for answers.
well, I switch to different movies of same data sets to start, still, it report the same error at the second loading. Should the corruption always happens at the second movie. Or the error relates to some memory problems?

4

Hi @Y_Z,

Is it possible if you can go to the folder where the raw data lives and ensure the file sizes are all the same size (down to the byte)? If one of them is different it might indicate that a file is corrupt. Please let us know!

5

Hi Everyone,

One potential cause for this error is a bug in cryoSPARC, and it has been fixed as of v2.15.0: