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Noble-Lab / casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
https://casanovo.readthedocs.io
Apache License 2.0
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Casanovo makes no predictions when n_beams = 1 #240

Closed justin-a-sanders closed 1 year ago

justin-a-sanders commented 1 year ago

On the current dev branch, when I run Casanovo in denovo with n_beams set to 1 casanovo makes no predictions and I get an empty output file. However, everything works as expected and I get predictions when n_beams > 1.

Here is the command I am running:

casanovo --mode=denovo --peak_path=../data/small_train_peps.mgf --output ../results/sanders_9-1-23/n_beams_test --config config.yaml

And here is the test dataset I experience the issue with: https://drive.google.com/file/d/1OJqlmKwr6g_2U6OLCfuqFt-EAqibd1NA/view?usp=sharing

wsnoble commented 1 year ago

This happened before:

https://github.com/Noble-Lab/casanovo/issues/185

justin-a-sanders commented 1 year ago

Was on wrong branch - inference with n_beams=1 works as expected on current dev branch.