Error import .eer format

Import and Export
1

Hi,

I am trying to import .eer files and keep getting the following error

Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 93, in cryosparc_compute.run.main
  File "/shared/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py", line 861, in run_import_movies_or_micrographs
    eer_upsamp_factor=eer_upsamp_factor)
  File "/shared/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py", line 687, in read_movie_header
    nz, ny, nx = eer.read_eer_shape(abs_path)
  File "/shared/cryosparc/cryosparc_master/cryosparc_compute/blobio/eer.py", line 18, in read_eer_shape
    eer = open_eer(fname)
  File "/shared/cryosparc/cryosparc_master/cryosparc_compute/blobio/eer.py", line 15, in open_eer
    return eerdecompressor.ElectronCountedFramesDecompressor(str(fname))
RuntimeError: unable to open tiff file

Any help would be appreciated!

Thanks,
Deirdre

2

Welcome to the forum @dcostello1.

Is this the end of that log file?
Please can you post any error message(s) that you may find in that job’s job.log file (guide).

3

Sure, please see below. Thank you!

CryoSPARC
CryoSPARC

00m 00s
Filter data



================= CRYOSPARCW =======  2022-10-31 22:46:20.627176  =========
Project P4 Job J13
Master 10.30.148.81 Port 45002
===========================================================================
========= monitor process now starting main process
MAINPROCESS PID 3843
========= monitor process now waiting for main process
MAIN PID 3843
imports.run cryosparc_compute.jobs.jobregister
ElectronCountedFramesDecompressor: reading using TIFF-EER mode.
/fsx/sdm1g22aug25h/frames/rawdata/sdm1g22aug25h_a_00002gr_00014sq_v02_00005hl_v01_00002fen4.frames.eer: Cannot read TIFF header
***************************************************************
**** handle exception rc
set status to failed
========= main process now complete.
========= monitor process now complete.
4

Could this file have been corrupted?
What is the output of

stat /fsx/sdm1g22aug25h/frames/rawdata/sdm1g22aug25h_a_00002gr_00014sq_v02_00005hl_v01_00002fen4.frames.eer

?

5

The stat output is below. The files were imported in Relion without any issues so I’m not sure if it’s file corruption

File: sdm1g22aug25h_a_00002gr_00014sq_v02_00005hl_v01_00002fen4.frames.eer
Size: 799221368 Blocks: 1560984 IO Block: 4096 regular file
Device: 2fh/47d Inode: 173951535607263497 Links: 1
Access: (0777/-rwxrwxrwx) Uid: ( 1000/dcostello) Gid: ( 1000/dcostello)
Access: 2022-11-01 15:17:43.161281800 -0700
Modify: 2022-11-01 15:17:43.161281800 -0700
Change: 2022-11-01 15:17:43.161281800 -0700
Birth: -

6

Would you be willing two EER example files, including this file, with us?