Local motion correction error: RuntimeError: unable to open tiff file

Troubleshooting
1

Hi all,

I’m having a problem with the local motion correction job in one of my projects, so this time I’m not lacking any patch or something like that.

So as I said, I have a project/workspace in which I could run the local motion correction job without any kind of problem after patching with the last update (it’s an EER dataset).
But in another project (same microscope, same settings everything, including box size, pixel size…) it just gives me the following error:

[CPU: 415.1 MB]  Traceback (most recent call last):
  File "/cephfs/vicente/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py", line 1791, in run_with_except_hook
    run_old(*args, **kw)
  File "/cephfs/vicente/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/threading.py", line 870, in run
    self._target(*self._args, **self._kwargs)
  File "/cephfs/vicente/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py", line 86, in stage_target
    work = processor.exec(item)
  File "/cephfs/vicente/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py", line 43, in exec
    return self.process(item)
  File "cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_local.py", line 134, in cryosparc_compute.jobs.motioncorrection.run_local.run_local_motion_correction_multi.motionworker.process
  File "cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_local.py", line 155, in cryosparc_compute.jobs.motioncorrection.run_local.run_local_motion_correction_multi.motionworker.process
  File "/cephfs/vicente/cryosparc/cryosparc_worker/cryosparc_compute/blobio/eer.py", line 86, in read_eer
    eer = open_eer(fname)
  File "/cephfs/vicente/cryosparc/cryosparc_worker/cryosparc_compute/blobio/eer.py", line 15, in open_eer
    return eerdecompressor.ElectronCountedFramesDecompressor(str(fname))
RuntimeError: unable to open tiff file

I tried re-extracting the particles, as I read that it might be the cause, but it didn’t help. I checked the particles integrity with the check for corrupt particles job, but nothing (also, the number of particles didn’t change).

Any ideas?
The workflow has been, in both instances:
(after particle extraction): (heterogenous refinement, homogeneous refinement legacy)x2, NU-refinement NEW, Local motion correction.

2

Hi @sente,

This probably means there’s a problem with one of the files in your dataset. Would you be able to post the last 50 or so lines of the job log? You can get the path the job log using the following command (replace xx and yy with the project and job number).

cryosparcm cli "get_job_log_path_abs('Pxx','Jyy')"

Then you can print out the last 50 lines with tail -50 /path/to/job/log

–Harris

3

Hi,

Thanks for your reply!

Indeed, the log was showing that there was a missing .EER file. After replacing the missing file I did some tests and now everything is working fine, so thanks so much!

(I really don’t know how or why the file is missing though, but it is what it is…)

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