No such file or directory: results

[DrJesseHansen]

Hi

I followed your tutorial steps except using my data. I gave it several tomograms, preprocessed as you describe, then ran refine on the HPC. It runs for about 3 minutes then throws an error cannot find Results/....

I am running isonet/0.2.

File "/mnt/nfs/clustersw/Debian/bullseye/cuda/11.2/isonet/0.2/IsoNet/bin/refine.py", line 114, in run
get_cubes_list(args)
File "/mnt/nfs/clustersw/Debian/bullseye/cuda/11.2/isonet/0.2/IsoNet/preprocessing/prepare.py", line 183, in get_cubes_list
p.map(func,inp)
File "/usr/lib/python3.9/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/usr/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: 'results/L1g4top2_ts_004_iter00.mrc'

I looked in the results folder and found results/L1g4top2_ts_004_iter00.mrc_17 (and other files with _17 ending for my other tomograms).

any suggestions are welcome!

thanks

Jesse

[procyontao]

Hi Jesse,

May I know whether this problem is reproducible?
Do you have any idea where "_17" come from? whether the name of your original tomograms somehow contains "_17"?

Best,
Yun-Tao

[jhennies]

Hi, I have the same issue.

I'll try to add a bit more information:

my tomograms are called WT_???.rec.mrc. The results folder then contains this when the error occurs:

• data/
• model_iter00.h5
• WT_001_iter00.rec_000000
• WT_001_iter00.rec_000001
• ... (and so forth for all tomograms)

The file required by the error message FileNotFoundError: [Errno 2] No such file or directory: 'results/WT_001_iter00.mrc' does indeed not exist.

I'm a bit surprised that it's not there as it should be produced here:
https://github.com/IsoNet-cryoET/IsoNet/blob/master/preprocessing/prepare.py#L224

which is supposedly called here:
https://github.com/IsoNet-cryoET/IsoNet/blob/master/bin/refine.py#L90

In the isonet code that I cloned these lines both exist, so I should have the correct version.

Any ideas? Anything that I could supply additionally?

Best,
Julian

[jhennies]

After renaming my files with only one "." before the file extension (e.g. WT_001.rec.mrc -> WT_001_rec.mrc) everything runs properly.

I'm assuming that Jesse might have been facing the same issue.

From my side this issue here is solved, however this one should be fixed: #52