ValueError: Map ID string not found - not an MRC file, or file is corrupt

[Sanjay Kumar]

Hi

Did anyone face this issue? I'm having this issue after running the final refine step. This is my command: isonet.py refine subtomo.star --gpuID 0 --iterations 30 --noise_start_iter 10,15,20,25 --noise_level 0.05,0.1,0.15,0.2

Error message:

Traceback (most recent call last):
  File "/home/rkhayat/Applications/IsoNet/bin/refine.py", line 115, in run
    get_cubes_list(args)
  File "/home/rkhayat/Applications/IsoNet/preprocessing/prepare.py", line 183, in get_cubes_list
    p.map(func,inp)
  File "/usr/lib/python3.8/multiprocessing/pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/usr/lib/python3.8/multiprocessing/pool.py", line 771, in get
    raise self._value
ValueError: Map ID string not found - not an MRC file, or file is corrupt

I checked my mrc files, and I didn't see any problems.

[YUNTAO LIU]

Hi Sanjay,

I checked the document for mrcfile: https://mrcfile.readthedocs.io/en/stable/usage_guide.html#permissive-read-mode. This "ValueError: Map ID string not found - not an MRC file, or file is corrupt" might be caused by incorrect headers.

I add "permissive=True" for all the "mrcfile.open" in the code, which will ignore this error. The latest commit on master branch on github should fix your problem. Could you please test it?

Best Regards,

Yuntao 

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Best Regards,

Yuntao Liu,  Postdoc.

California NanoSystem Institute

University of California Los Angeles

[Sanjay Kumar]

Hi,

I tested it and it worked fine. To check which my mrc file has a problem, I split my data into small sets like 10 tiltseries for each 5 test sets and the strange thing is that none of them showed any error, it worked fine. when i increase 10 to 15 or 20, it showed the same error. I don't know why this is happening. By the way, my problem was solved, many thanks.

Thanks,

Sanjay

[YUNTAO LIU]

Glad it worked! We typically do not use too many tomograms for IsoNet refine. 5-10 should be enough.

[Sanjay Kumar]

Thanks for the clarification.