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weberlab-hhu / Helixer

Using Deep Learning to predict gene annotations
GNU General Public License v3.0
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Overlapping does not work with --chunk-size 19440 #58

Open soi opened 3 years ago

soi commented 3 years ago

./DanQModel.py -v -l /mnt/data/felix/nni-experiments/7SYI4tA8/trials/ppoJD/best_model.h5 --pool-size 9 --predict-phase --val-test-batch-size 400 --eval -t /tmp/tmp.Y4LbBg7TLq/crein.h5 --overlap --overlap-offset 3240

Traceback (most recent call last): File "./DanQModel.py", line 165, in model.run() File "/home/felix/git/Helixer/helixer/prediction/HelixerModel.py", line 752, in run , , _ = HelixerModel.run_metrics(test_generator, model, calc_H=self.calculate_uncertainty) File "/home/felix/git/Helixer/helixer/prediction/HelixerModel.py", line 478, in run_metrics metrics = metrics_calculator.calculate_metrics(model) File "/home/felix/git/Helixer/helixer/prediction/Metrics.py", line 260, in calculate_metrics cm.count_and_calculate_one_batch(y_true, y_pred, sw) File "/home/felix/git/Helixer/helixer/prediction/Metrics.py", line 64, in count_and_calculate_one_batch y_true, y_pred = ConfusionMatrix._remove_masked_bases(y_true, y_pred, sw) File "/home/felix/git/Helixer/helixer/prediction/Metrics.py", line 31, in _remove_masked_bases y_true = y_true[sw] IndexError: boolean index did not match indexed array along dimension 0; dimension is 65 but corresponding boolean dimension is 64