Open DrJesseHansen opened 1 year ago
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
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:
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
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
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