Dear IsoNet team,
I followed the download instructions as described on the GitHub.
I enter the following error messages when I run the bash install.sh command
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed.
This behaviour is the source of the following dependency conflicts. scikit-image 0.25.2 requires lazy-loader>=0.4, but you have lazy-loader 0.3 which is incompatible. wheel 0.46.3 requires packaging>=24.0, but you have packaging 23.2 which is incompatible.
Processing ./.
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: IsoNet2
Building wheel for IsoNet2 (pyproject.toml) ... done
Created wheel for IsoNet2: filename=isonet2-2.0.1b0-py3-none-any.whl size=2401859 sha256=7e2892aada88a44e93ff2a331a0963170e3493f8cc96f71c016cba6e7eb08028
Stored in directory: /tmp/pip-ephem-wheel-cache-1achogux/wheels/89/3d/96/a39ba125a4e956e94e4474e3a63c35b580b715f448bd74c027
Successfully built IsoNet2
Installing collected packages: IsoNet2
Successfully installed IsoNet2-2.0.1b0
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 154M 100 154M 0 0 187M 0 --:--:-- --:--:-- --:--:-- 290M
So I checked the isonet2_environment.yml file in order to see which dependencies are needed, and I see the following lines:
scikit-image
lazy-loader==0.3
packaging==23.2
Those are the same versions the installation error was complaining about. Further I sources the isonet2.bashrc file - However I am not able to activate the conda environment.
Some of the commands are still working fine, I tried prepare_star, deconv and make mask. If i try to run refine, the following issue appears:
isonet.py refine tomograms.star --method isonet2-n2n --cube_size 128 --epochs 70 --mw_weight 200 --CTF_mode network --bfactor 200 --gpuID 0
02-03 10:42:16, INFO 16 CPU cores per GPU, total 16 CPUs
02-03 10:42:16, INFO Enabling mw_weight
02-03 10:42:16, INFO Total number of parameters: 23989825
02-03 10:42:16, INFO Port number: 46933
Preprocess tomograms: 0%| | 0/11 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/home/cemkguest/software/IsoNet2/build/conda_env/bin/isonet.py", line 6, in <module>
sys.exit(main())
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/IsoNet/bin/isonet.py", line 1064, in main
fire.Fire(ISONET)
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/fire/core.py", line 475, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/fire/core.py", line 691, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/IsoNet/bin/isonet.py", line 743, in refine
network.prepare_train_dataset(training_params)
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/IsoNet/models/network.py", line 168, in prepare_train_dataset
self.train_dataset = Train_sets_n2n(training_params['star_file'],method=training_params['method'],
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/IsoNet/models/data_sequence.py", line 128, in __init__
self._initialize_data()
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/IsoNet/models/data_sequence.py", line 144, in _initialize_data
mask = self._load_statistics_and_mask(row, column_name_list)
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/IsoNet/models/data_sequence.py", line 185, in _load_statistics_and_mask
with mrcfile.mmap(row[even_column], mode='r', permissive=True) as tomo_even, \
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/mrcfile/load_functions.py", line 274, in mmap
return MrcMemmap(name, mode=mode, permissive=permissive)
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/mrcfile/mrcfile.py", line 109, in __init__
self._open_file(name)
File "/home/cemkguest/software/IsoNet2/build/conda_env/lib/python3.10/site-packages/mrcfile/mrcfile.py", line 126, in _open_file
self._iostream = open(name, self._mode + 'b')
FileNotFoundError: [Errno 2] No such file or directory: 'None'
The traceback points to:
with mrcfile.mmap(row[even_column], mode='r', permissive=True)
This suggests that a file path from the STAR file is being read as None (I am using full tomograms) . Could the refine error be related to the environment inconsistencies, or does it indicate a formatting/path issue in the STAR file? Is there a recommended way to correctly activate or recreate the IsoNet2 conda environment?
I would appreciate any help!
Best,
Tamino
Dear IsoNet team,
I followed the download instructions as described on the GitHub.
I enter the following error messages when I run the bash install.sh command
So I checked the
isonet2_environment.ymlfile in order to see which dependencies are needed, and I see the following lines:Those are the same versions the installation error was complaining about. Further I sources the isonet2.bashrc file - However I am not able to activate the conda environment.
Some of the commands are still working fine, I tried prepare_star, deconv and make mask. If i try to run refine, the following issue appears:
The traceback points to:
with mrcfile.mmap(row[even_column], mode='r', permissive=True)This suggests that a file path from the STAR file is being read as None (I am using full tomograms) . Could the refine error be related to the environment inconsistencies, or does it indicate a formatting/path issue in the STAR file? Is there a recommended way to correctly activate or recreate the IsoNet2 conda environment?
I would appreciate any help!
Best,
Tamino