Micrographs import error

Hi,
We are trying to import motioncerrected micrographs from Relion3.1 on superresolution movies. We are getting following error:

[CPU: 245.0 MB]  Traceback (most recent call last):
  File "cryosparc2_master/cryosparc2_compute/run.py", line 82, in cryosparc2_compute.run.main
  File "cryosparc2_compute/jobs/imports/run.py", line 661, in run_import_movies_or_micrographs
    imgdata = mrc.read_mrc(os.path.join(proj_dir_abs, exp['micrograph_blob/path']))[1][0]
IndexError: index 0 is out of bounds for axis 0 with size 0

Can anyone please suggest any solution to overcome this issue.

Thanks, Shashi

Hi @sbhushan,

Which version of cryoSPARC are you running?
Can you provide more information about the movie file - if you do
du
on the directory with the movie files, what size are they?
The error indicates that the file was read and it’s header was read, but the data is empty.

Dear Apunjani,

we are using v2.14.2.

These are motioncorrected micrographs from relion3.1.

this is the result of ls -ltr to show that files are not empty.

rwxrwxrwx. 1 shashi shashi 56956944 Jul 21 11:33 FoilHole_7837481_Data_7801966_7801968_20200710_142136-205399.mrc
-rwxrwxrwx. 1 shashi shashi 56956944 Jul 21 11:33 FoilHole_7832167_Data_7801966_7801968_20200709_214552-204500.mrc

this from du
[shashi@172 Micrographs]$ du
136501540

Header shows;

[shashi@172 Micrographs]$ header FoilHole_7840182_Data_7801966_7801968_20200710_230540-205877.mrc

RO image file on unit 1 : FoilHole_7840182_Data_7801966_7801968_20200710_230540-205877.mrc Size= 55622 K

Number of columns, rows, sections … 3838 3710 1
Map mode … 2 (32-bit real)
Start cols, rows, sects, grid x,y,z … 0 0 0 3838 3710 1
Pixel spacing (Angstroms)… 0.8600 0.8600 0.8600
Cell angles … 90.000 90.000 90.000
Fast, medium, slow axes … X Y Z
Origin on x,y,z … 0.000 0.000 0.000
Minimum density … 6.0067
Maximum density … 8.6468
Mean density … 7.1053
RMS deviation from mean… 0.0000
tilt angles (original,current) … 0.0 0.0 0.0 90.0 90.0 90.0
Space group,# extra bytes,idtype,lens . 0 0 5 0

 0 Titles :

Thanks. Shashi