bittremieux / gleams Goto Github PK
View Code? Open in Web Editor NEWGLEAMS is a Learned Embedding for Annotating Mass Spectra.
Home Page: https://doi.org/10.1101/483263
License: BSD 3-Clause "New" or "Revised" License
GLEAMS is a Learned Embedding for Annotating Mass Spectra.
Home Page: https://doi.org/10.1101/483263
License: BSD 3-Clause "New" or "Revised" License
Hi Wout,
I received this error while running gleams embed: gleams_error.txt
Any advice on how to resolve this? The server I am using does not have GPU access, but I will switch to a server with GPU soon. But I wasn't sure that this was a problem that was GPU related?
Thanks,
Kevin
I used the reference mgf with 1000 PSM, while it only output 968 embedding. Could you please share the information about the missing PSM?
I was trying to execute gleams embed as it is provided in your instructions. However, I am facing the below OSError saying that the saved model in .pbtxt or .pb format is not present in the said path.
**2022-12-03 15:10:00,264 INFO [gleams/MainProcess] gleams.cli_embed : GLEAMS version 0.4.dev1+g8831ad6
2022-12-03 15:10:00,282 DEBUG [gleams/MainProcess] encoder.__init__ : Read the reference spectra
2022-12-03 15:10:00,907 DEBUG [gleams/MainProcess] encoder.__init__ : Select 500 valid reference spectra
2022-12-03 15:10:03,207 DEBUG [gleams/MainProcess] nn.embed : Load the stored GLEAMS neural network
2022-12-03 15:10:04,047 DEBUG [gleams/MainProcess] embedder.__init__ : Running the embedder model on 1 GPU(s)
Traceback (most recent call last):
File "/home/hp/miniconda3/envs/gleams/bin/gleams", line 8, in <module>
sys.exit(gleams())
File "/home/hp/miniconda3/envs/gleams/lib/python3.8/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/home/hp/miniconda3/envs/gleams/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/hp/miniconda3/envs/gleams/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/hp/miniconda3/envs/gleams/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/hp/miniconda3/envs/gleams/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/home/hp/miniconda3/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 "/home/hp/miniconda3/envs/gleams/lib/python3.8/site-packages/gleams/nn/nn.py", line 163, in embed
emb.load()
File "/home/hp/miniconda3/envs/gleams/lib/python3.8/site-packages/gleams/nn/embedder.py", line 158, in load
self.siamese_model = keras.models.load_model(self.filename)
File "/home/hp/miniconda3/envs/gleams/lib/python3.8/site-packages/tensorflow/python/keras/saving/save.py", line 186, in load_model
loader_impl.parse_saved_model(filepath)
File "/home/hp/miniconda3/envs/gleams/lib/python3.8/site-packages/tensorflow/python/saved_model/loader_impl.py", line 110, in parse_saved_model
raise IOError("SavedModel file does not exist at: %s/{%s|%s}" %
OSError: SavedModel file does not exist at: /home/hp/miniconda3/envs/gleams/gleams/data/gleams_82c0124b.hdf5/{saved_model.pbtxt|saved_model.pb}
The error is because any package is missing in the conda environment where gleams has been installed?
--
Chinmaya
Thanks for sharing this great work. I think GLEAMS is very helpful for processing the mass spectrum.
However, when I am checking the datasets used in GLEAMS, I cannot find how to download the 30 million high-quality PSMs of the MassIVE-KB spectral library and 185 million PSMs of the identification results for the full MassIVE-KB dataset in the MassIVE web site. Could you kindly help me about how to find these data?
Looking forward to your reply.
Hi,
I have an MGF file with 10,067 spectra in it, but running gleams embed
only returns embeddings for 1,663 of them. Any idea why?
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
Hello,
I have installed the GLEAMS tool in one of my conda env. I am planning to check MS/MS clusters specific to data from different species. However, the general gleams command execution shows only embed and cluster options for mzML input files. It is not clear whether the embedding has to be done together for all the mzML files from all the species or it has to be done separately and clustered together at the "gleams cluster" step?.
Please help
Thanks,
Chinmaya
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.