Open Chrisvanhoorn opened 2 years ago
Hi,
We ran into this problem before, it was because the tomogram file name contains a dot sign. Please tell me whether this is also your case.
That fixed it! thank you
quick script which I used to fix this for my subtomo filenames which included two leading '.' characters, might save someone some time
import starfile
import os
star = starfile.read('subtomo.star')
for src, dest in zip (star['rlnImageName'], star['rlnImageName'].str.replace('.','_', 2)):
os.symlink(src, dest)
star['rlnImageName'] = star['rlnImageName'].str.replace('.','_', 2)
starfile.write(star, 'subtomo_nodot.star')
I'm still running into this at the refinement step despite the subtomo names having no dots.
To be clear:
subtomo.star
file and symlink the files with the script above
-I run isonet.py refine subtomo_nodot.star --gpuID 0,1,2,3 --iterations 30 --noise_start_iter 10,15,20,25 --noise_level 0.05,0.1,0.15,0.2
Traceback (most recent call last):
File "/lmb/home/aburt/isonet/IsoNet/bin/refine.py", line 25, in run
run_whole(args)
File "/lmb/home/aburt/isonet/IsoNet/bin/refine.py", line 109, in run_whole
args = prepare_first_iter(args)
File "/lmb/home/aburt/isonet/IsoNet/preprocessing/prepare.py", line 115, in prepare_first_iter
res = p.map(func, settings.mrc_list)
File "/lmb/home/aburt/mambaforge/envs/isonet/lib/python3.8/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/lmb/home/aburt/mambaforge/envs/isonet/lib/python3.8/multiprocessing/pool.py", line 771, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: 'subtomo/TS_009_mrc_8_80Apx_000000.mrc'
(isonet) hal.lmb.internal ➜ isonet ls subtomo/TS_009_mrc_8_80Apx_000000.mrc
subtomo/TS_009_mrc_8_80Apx_000000.mrc
Hi alisterburt,
I sorry that I just noticed you message have not been replied. People recently are still complaining about similar file not found error. I wonder whether this problem still exists in your case?
And thank you for your suggestion for fixing the issue related to '.' characters.
Best, Yuntao
Hi all,
I am running into an issue during the refinement stage. I have all the dependencies installed with the right version according to the tensorflow table:
Python 3.7.11 Tensor flow 2.6.2 cuDNN 8.1.0.77-h90431f1_0 CUDA 11.2
Would you know what is causing the following error? many thanks!