FileNotFoundError with conll_output_filepath

I’m trying to follow the steps from the README to run NeuroNER using the default parameters.ini settings. I’m running into a FileNotFoundError at train.py, line 95.

I’m new to python, but will try to track down the source of the issue. It looks like maybe the file should’ve been created by this line, but it’s not clear to me why.

This is on ubuntu 16.04, python 3.5.2. Any advice on how to debug this issue?

Here’s partial output from running python main.py:

Starting epoch 0
Training completed in 0.00 seconds
Evaluate model on the train set
Traceback (most recent call last):
  File "main.py", line 445, in <module>
    main()
  File "main.py", line 392, in main
    y_pred, y_true, output_filepaths = train.predict_labels(sess, model, transition_params_trained, parameters, dataset, epoch_number, stats_graph_folde$
, dataset_filepaths)
  File "/home/user/neuroner/neuroner/src/train.py", line 113, in predict_labels
    prediction_output = prediction_step(sess, dataset, dataset_type, model, transition_params_trained, stats_graph_folder, epoch_number, parameters, dat$
set_filepaths)
  File "/home/user/neuroner/neuroner/src/train.py", line 95, in prediction_step
    with open(conll_output_filepath, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '../output/en_2017-07-05_22-35-05-549137/000_train.txt_conll_evaluation.txt'

[davidbenton]

This was a memory error. The perl script wasn’t able to complete because of insufficient memory, but os.system hides the error output. I increased the swapfile size and all’s well.

[nader2929]

I am also running into the same issue however I am running POP_OS! which uses btfrs, so increasing the swapfile size is a bit problematic.

Formatting deploy set from BRAT to CONLL... Done.
Converting CONLL from BIO to BIOES format... Done.
Predict labels for the deploy set
Formatting 006_deploy set from CONLL to BRAT... Done.
Traceback (most recent call last):
  File "neuroner_starter_code.py", line 124, in <module>
    load_neuroner()    
  File "neuroner_starter_code.py", line 79, in load_neuroner
    nn.predict(fileTxt)
  File "/home/wdps/.local/lib/python3.7/site-packages/neuroner/neuromodel.py", line 813, in predict
    annotation_filepath, verbose=True)
  File "/home/wdps/.local/lib/python3.7/site-packages/neuroner/brat_to_conll.py", line 73, in get_entities_from_brat
    with codecs.open(text_filepath, 'r', 'UTF-8') as f:
  File "/usr/lib/python3.7/codecs.py", line 898, in open
    file = builtins.open(filename, mode, buffering)
FileNotFoundError: [Errno 2] No such file or directory: './output/temp_2021-11-19_00-25-04-988634/brat/deploy/temp_00006.txt'

This is the stack trace, any guidance from anyone would be appreciated. Any more needed info let me know.

Thank you

So realised that some of my text files are empty which also causes this error. Adding a check for that got rid of the error.