ValueError: invalid literal for int() with base 10

[nattzy94]

Hi I am running GLEAMS on a bunch of MGF files using gleams embed *.mgf --embed_name GLEAMS_embed with 1 gpu.

The job starts:

2023-10-18 23:08:17,623 INFO [gleams/MainProcess] gleams.cli_embed : GLEAMS version 0.4.dev7+g13ebc74.d20231018
2023-10-18 23:08:17,672 DEBUG [gleams/MainProcess] encoder.init : Read the reference spectra
2023-10-18 23:08:18,008 DEBUG [gleams/MainProcess] encoder.init : Select 500 valid reference spectra
2023-10-18 23:08:19,146 DEBUG [gleams/MainProcess] nn.embed : Load the stored GLEAMS neural network
2023-10-18 23:08:19,200 DEBUG [gleams/MainProcess] embedder.init : Running the embedder model on 1 GPU(s)
2023-10-18 23:08:19,660 INFO [gleams/MainProcess] nn.embed : Embed all peak files for metadata file /var/tmp/pbs.858407.hn-10-03/tmpy7q23kig/GLEAMS_embed.parquet
2023-10-18 23:08:19,662 INFO [gleams/MainProcess] nn.embed : Process dataset GLEAMS [ 1/ 1] (120 files)
2023-10-18 23:08:19,663 DEBUG [gleams/MainProcess] feature._peaks_to_features : Process file 202112249_TY_Nathaniel_1364_m2_3_FAIMS_OTIT_F1.mgf

but then encounters the following error:

Traceback (most recent call last):
  File "/data/petretto/home/e0470749/.conda/envs/gleams/bin/gleams", line 8, in <module>
    sys.exit(gleams())
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/gleams/gleams.py", line 97, in cli_embed
    nn.embed(metadata_filename, config.model_filename, f'{embed_name}.npy',
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/gleams/nn/nn.py", line 188, in embed
    for filename, file_scans, file_encodings in joblib.Parallel(
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/joblib/parallel.py", line 1041, in __call__
    if self.dispatch_one_batch(iterator):
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/joblib/parallel.py", line 859, in dispatch_one_batch
    self._dispatch(tasks)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/joblib/parallel.py", line 777, in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/joblib/_parallel_backends.py", line 208, in apply_async
    result = ImmediateResult(func)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/joblib/_parallel_backends.py", line 572, in __init__
    self.results = batch()
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/joblib/parallel.py", line 262, in __call__
    return [func(*args, **kwargs)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/joblib/parallel.py", line 262, in <listcomp>
    return [func(*args, **kwargs)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/gleams/feature/feature.py", line 68, in _peaks_to_features
    scans['scan'] = scans['scan'].astype(np.int64)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/pandas/core/generic.py", line 5815, in astype
    new_data = self._mgr.astype(dtype=dtype, copy=copy, errors=errors)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/pandas/core/internals/managers.py", line 418, in astype
    return self.apply("astype", dtype=dtype, copy=copy, errors=errors)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/pandas/core/internals/managers.py", line 327, in apply

[nattzy94]

Hi, I converted my mgf to mzML using msconvert and reran gleam embed on the mzML file:

gleams embed *.mzML --embed_name GLEAMS_embed

However, I run into the following error:

Traceback (most recent call last):
  File "/data/petretto/home/e0470749/.conda/envs/gleams/bin/gleams", line 8, in <module>
    sys.exit(gleams())
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/gleams/gleams.py", line 97, in cli_embed
    nn.embed(metadata_filename, config.model_filename, f'{embed_name}.npy',
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/gleams/nn/nn.py", line 220, in embed
    _combine_embeddings(
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/gleams/nn/nn.py", line 290, in _combine_embeddings
    np.save(filename_embeddings, np.vstack(embeddings))
  File "<__array_function__ internals>", line 5, in vstack
  File "/data/petretto/home/e0470749/.conda/envs/gleams/lib/python3.8/site-packages/numpy/core/shape_base.py", line 283, in vstack
    return _nx.concatenate(arrs, 0)
  File "<__array_function__ internals>", line 5, in concatenate
ValueError: need at least one array to concatenate

2023-11-10 13:37:11,224 INFO [gleams/MainProcess] gleams.cli_embed : GLEAMS version 0.4.dev7+g13ebc74.d20231018
2023-11-10 13:37:11,242 DEBUG [gleams/MainProcess] encoder.__init__ : Read the reference spectra
2023-11-10 13:37:11,570 DEBUG [gleams/MainProcess] encoder.__init__ : Select 500 valid reference spectra
2023-11-10 13:37:12,706 DEBUG [gleams/MainProcess] nn.embed : Load the stored GLEAMS neural network
2023-11-10 13:37:12,747 DEBUG [gleams/MainProcess] embedder.__init__ : Running the embedder model on 1 GPU(s)
2023-11-10 13:37:13,191 INFO [gleams/MainProcess] nn.embed : Embed all peak files for metadata file /var/tmp/pbs.864605.hn-10-03/tmp584gx28f/GLEAMS_embed.parquet
2023-11-10 13:37:13,192 INFO [gleams/MainProcess] nn.embed : Process dataset GLEAMS [  1/  1] (1 files)
2023-11-10 13:37:13,193 DEBUG [gleams/MainProcess] feature._peaks_to_features : Process file 20210331_TY_GndHCL_Extract2_C18_F1.mzML
2023-11-10 13:37:34,114 INFO [gleams/MainProcess] nn._combine_embeddings : Combine embeddings for 1 datasets
2023-11-10 13:37:34,114 DEBUG [gleams/MainProcess] nn._combine_embeddings : Append dataset GLEAMS [  1/  1]
2023-11-10 13:37:34,115 WARNING [gleams/MainProcess] nn._combine_embeddings : Missing embeddings for dataset GLEAMS, skipping...

I'm not really sure what is happening here. Is there a problem with writing out the embeddings?

[JannikSchneider12]

Hey, I have the same error. Did you found a solution?

[nattzy94]

Unfortunately no, haven't been able to solve this.

[TIKeng]

You can change TITLE=mzspec:MSV000080225:HUVEC_ne_con_5b_1:scan:20120 into TITLE=1.