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Hi, I run into the following error while trying to run some simulated dataset. We have several settings, and two settings gave us the same error regardless of parameters settings.
100%|██████████| 166314/166314 [00:00<00:00, 309719.43it/s]
generating start/end dict for chromosome
extracting from data.txt
generating contact maps for baseline
data loaded
166314 False
creating matrices tasks: 100%|██████████| 1/1 [00:00<00:00, 2.69it/s]
100%|██████████| 1/1 [00:00<00:00, 20.34it/s]
0.608: 100%|██████████| 300/300 [00:00<00:00, 300.39it/s]
100%|██████████| 1/1 [00:00<00:00, 46091.25it/s]
100%|██████████| 1/1 [00:00<00:00, 54471.48it/s]
total_feats_size 80
cpu_num 1
setting to gpu:0
training on data from: ['chr1']
total_sparsity_cell 0.8946236559139785
contractive loss
batch_size 256
Node type num [100 61] [100 161]
start making attribute
loss 0.6080093383789062 loss best 0.6089616417884827 epochs 299
initializing data generator
initializing data generator
First stage training
[ Epoch 0 of 60 ]
- (Training) : 0%| | 0/1000 [00:00<?, ?it/s]concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/.conda/envs/higashi/lib/python3.9/concurrent/futures/process.py", line 243, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/.conda/envs/higashi/lib/python3.9/site-packages/higashi-0.1.0a0-py3.9.egg/higashi/Higashi_wrapper.py", line 248, in one_thread_generate_neg
raise EOFError
EOFError
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Data/run_higashi.py", line 10, in <module>
higashi_model.train_for_embeddings()
File "/.conda/envs/higashi/lib/python3.9/site-packages/higashi-0.1.0a0-py3.9.egg/higashi/Higashi_wrapper.py", line 1336, in train_for_embeddings
self.train(
File "/.conda/envs/higashi/lib/python3.9/site-packages/higashi-0.1.0a0-py3.9.egg/higashi/Higashi_wrapper.py", line 1113, in train
bce_loss, mse_loss, train_accu, auc1, auc2, str1, str2, train_pool, train_p_list = self.train_epoch(
File "/.conda/envs/higashi/lib/python3.9/site-packages/higashi-0.1.0a0-py3.9.egg/higashi/Higashi_wrapper.py", line 914, in train_epoch
batch_edge_big, batch_y_big, batch_edge_weight_big, batch_chrom_big, batch_to_neighs_big, chroms_in_batch = p.result()
File "/.conda/envs/higashi/lib/python3.9/concurrent/futures/_base.py", line 438, in result
return self.__get_result()
File "/.conda/envs/higashi/lib/python3.9/concurrent/futures/_base.py", line 390, in __get_result
raise self._exception
EOFError
I did a little debugging myself, and for the runs that failed (very early into training), len(neg_list) (line 248 ish in Higashi_wrapper.py) usually is <5. In runs that didn't fail, it's usually around 100.
The text was updated successfully, but these errors were encountered:
Hi, I run into the following error while trying to run some simulated dataset. We have several settings, and two settings gave us the same error regardless of parameters settings.
The JSON input:
I did a little debugging myself, and for the runs that failed (very early into training), len(neg_list) (line 248 ish in Higashi_wrapper.py) usually is <5. In runs that didn't fail, it's usually around 100.
The text was updated successfully, but these errors were encountered: