Assertion Error: standardize_mrc did not get any inputs

[Srichnew]

Hi there,

I've been working on installing model angelo and noted a few things. For context, I'm working on installing it on a cluster using mamba. I found that while doing this, some of the code in the residue_constants.py file within python3.9/site-packages/model_angelo-0.2.3-py3.9.egg/model_angelo/utils was trying to use deprecated Numpy code, I have since altered the code based on the information provided by Numpy (see attached). residue_constants.txt

This was the first issue, and was reasonably easy to fix. Following this fix, I was able to start the program using "model_angelo -h", though when I actually try to run the build_no_seq command with a specified --volume-path, I receive the following error:

2023-04-05 at 12:31:23 | INFO | ModelAngelo with args: {'volume_path': '/stor1/data/model_angelo_data/test/cryosparc_p163_J37_005_volume_map_sharp.mrc', 'output_dir': '/stor1/data/model_angelo_data/test/test-output', 'mask_path': None, 'device': 'cuda:> 2023-04-05 at 12:31:23 | INFO | Input volume preprocessing with args: {'target_voxel_size': 1.5, 'crop_z': 0, 'bfactor_to_apply': 0, 'auto_mask': False, 'input_path': '/stor1/data/model_angelo_data/test/cryosparc_p163_J37_005_volume_map_sharp.mrc', 'ou> 2023-04-05 at 12:31:23 | ERROR | Error in ModelAngelo Traceback (most recent call last):

File "/apps/mamba/envs/model_angelo/bin/model_angelo", line 33, in sys.exit(load_entry_point('model-angelo==0.2.3', 'console_scripts', 'model_angelo')()) │ │ └ <function importlib_load_entry_point at 0x7fc12cf080d0> │ └ └ <module 'sys' (built-in)> File "/apps/mamba/envs/model_angelo/lib/python3.9/site-packages/model_angelo-0.2.3-py3.9.egg/model_angelo/main.py", line 51, in main args.func(args) │ │ └ Namespace(volume_path='/stor1/data/model_angelo_data/test/cryosparc_p163_J37_005_volume_map_sharp.mrc', output_dir='/stor1/da... │ └ <function main at 0x7fbe5e1b7160> └ Namespace(volume_path='/stor1/data/model_angelo_data/test/cryosparc_p163_J37_005_volume_map_sharp.mrc', output_dir='/stor1/da...

File "/apps/mamba/envs/model_angelo/lib/python3.9/site-packages/model_angelo-0.2.3-py3.9.egg/model_angelo/apps/build_no_seq.py", line 164, in main assert (

AssertionError: standardize_mrc did not get any inputs: /stor1/data/model_angelo_data/test/cryosparc_p163_J37_005_volume_map_sharp.mrc

I'm not really sure what I need to do here. I'm guessing its an issue of file format or something to do with my syntax in terms of defining the .mrc file's path, but regardless I am very confused. Any assistance would be greatly appreciated.

Thanks, Shane

[jamaliki]

Hi! If I had to guess, it would be that the machine you are running the program on doesn't have the "/stor1" directory mounted. Are you able to check that you can access this file outside of ModelAngelo?

[Srichnew]

Hi! I actually resolved the issue by running the command in the folder containing the file. I then had to alter the numpy code language in the "grid.py" file within the utils folder (just as an update).

[jamaliki]

Hmm, which part did you change? BTW, with the release of ModelAngelo-1.0 in a couple of weeks, a lot of this is going to be much simpler :)

[Srichnew]

Basically the same deprecated numpy code was the problem. Need to change all "np.int" to "int" and change all "np.float/np.float32" to "float". I went through and checked the code to see if any other deprecated numpy types were present (https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations). Thankfully though, it was just the np.int and np.float/np.float32 that needed changing. I think there were only a total of 5-8 of each. "np.float32" actually works, but "float" is the new name.

grid.txt

[jamaliki]

Awesome! Yes I had already realized this for ModelAngelo-1.0, which will be out soon. So, you don't mind if I close this issue now?

[Srichnew]

Sounds good! Great software btw! Very cool and it really does a great job.