michal-g
commented
2 weeks ago Hi Alana, can you double-check the version of cryoDRGN you have installed (using the command cryodrgn --version) and also the version of Python you are using? It looks like you may have some older versions for each (v0.3.3 and v3.7).
Another thing to double-check is if there are indeed degenerate values in your latent space matrix, which you can look at using something like the following:
import numpy as np
from cryodrgn.utils impoirt load_pkl
z = load_pkl("02_256_8D_1024/z.49.pkl")
np.isnan(z).sum()Generally the number of particles shouldn't be a problem in and of itself if the reconstruction already ran to completion, but the model might have had trouble coming up with a coherent representation of the heterogeneity landscape characterizing your input, leading to missing/null values in the model output.
Best, Michal
Alana-Cowell
Heya,
When I try to run cryodrgn analyze on my higher resolution dataset (256) I am getting the below error.
2024-10-02 12:10:55 Perfoming principal component analysis... Traceback (most recent call last): File "/s/ems/s/anaconda/v4.8.4/envs/cryodrgn_v3.3/bin/cryodrgn", line 33, in
sys.exit(load_entry_point('cryodrgn==0.3.3', 'console_scripts', 'cryodrgn')())
File "/s/ems/s/anaconda/v4.8.4/envs/cryodrgn_v3.3/lib/python3.7/site-packages/cryodrgn-0.3.3-py3.7.egg/cryodrgn/main.py", line 54, in main
args.func(args)
File "/s/ems/s/anaconda/v4.8.4/envs/cryodrgn_v3.3/lib/python3.7/site-packages/cryodrgn-0.3.3-py3.7.egg/cryodrgn/commands/analyze.py", line 190, in main
analyze_zN(z, outdir, vg, skip_umap=args.skip_umap, num_pcs=args.pc, num_ksamples=args.ksample)
File "/s/ems/s/anaconda/v4.8.4/envs/cryodrgn_v3.3/lib/python3.7/site-packages/cryodrgn-0.3.3-py3.7.egg/cryodrgn/commands/analyze.py", line 64, in analyze_zN
pc, pca = analysis.run_pca(z)
File "/s/ems/s/anaconda/v4.8.4/envs/cryodrgn_v3.3/lib/python3.7/site-packages/cryodrgn-0.3.3-py3.7.egg/cryodrgn/analysis.py", line 34, in run_pca pca.fit(z) File "/s/ems/s/anaconda/v4.8.4/envs/cryodrgn_v3.3/lib/python3.7/site-packages/sklearn/decomposition/_pca.py", line 382, in fit self._fit(X) File "/s/ems/s/anaconda/v4.8.4/envs/cryodrgn_v3.3/lib/python3.7/site-packages/sklearn/decomposition/_pca.py", line 431, in _fit X, dtype=[np.float64, np.float32], ensure_2d=True, copy=self.copy File "/s/ems/s/anaconda/v4.8.4/envs/cryodrgn_v3.3/lib/python3.7/site-packages/sklearn/base.py", line 561, in _validate_data X = check_array(X, **check_params) File "/s/ems/s/anaconda/v4.8.4/envs/cryodrgn_v3.3/lib/python3.7/site-packages/sklearn/utils/validation.py", line 792, in check_array _assert_all_finite(array, allow_nan=force_all_finite == "allow-nan") File "/s/ems/s/anaconda/v4.8.4/envs/cryodrgn_v3.3/lib/python3.7/site-packages/sklearn/utils/validation.py", line 116, in _assert_all_finite type_err, msg_dtype if msg_dtype is not None else X.dtype ValueError: Input contains NaN, infinity or a value too large for dtype('float32').
Command used is cryodrgn analyze 02_256_8D_1024 49 --Apix 1.08
I have over 500,000 particles so I'm wondering if that might be the issue? Or whether this might be related to the Assertion error people have been mentioning. Any suggestions on the cause and fix would be appreciated.
Thanks Alana