search

kusterlab / prosit

Prosit offers high quality MS2 predicted spectra for any organism and protease as well as iRT prediction. When using Prosit is helpful for your research, please cite "Gessulat, Schmidt et al. 2019" DOI 10.1038/s41592-019-0426-7
https://www.proteomicsdb.org/prosit/
Apache License 2.0
85 stars 45 forks source link

Expected time for job completion on server, and related feature request #78

Closed yangkl96 closed 2 years ago

yangkl96 commented 2 years ago

Hello,

I submitted two jobs yesterday to the Prosit server. It has been around 24 hours but they have not completed yet. How long can I typically expect it to take for a job to complete?

On a related note, would it be possible for the webpage to update with how many jobs are before mine in the queue?

Thanks, Kevin

WassimG commented 2 years ago

Can you send your Job id to let you know when it will finish?

yangkl96 commented 2 years ago

AD9D0EDADF1BEA157EFCEEFEFC608608 and A935DEDA956F184C3761E7A24E239F40

yangkl96 commented 2 years ago

My first job failed with the following error log. Could you explain what the issue was here?

2022-01-20 14:23:49.127235: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2022-01-20 14:23:49.127267: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. /root/oktoberfest/spectral_library.py:94: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy library.spectra_data['GRPC_SEQUENCE'] = library.spectra_data['MODIFIED_SEQUENCE'] 2022-01-20 14:23:53,986 - ERROR - oktoberfest.spectral_library::grpc_predict An exception was thrown! Traceback (most recent call last): File "/root/oktoberfest/spectral_library.py", line 96, in grpc_predict predictions,sequences = predictor.predict(sequences=library.spectra_data["GRPC_SEQUENCE"].values.tolist(), File "/usr/local/lib/python3.8/site-packages/prosit_grpc/predictPROSIT.py", line 152, in predict pred_object.predict(disable_progress_bar) AttributeError: 'NoneType' object has no attribute 'predict' Traceback (most recent call last): File "/usr/local/lib/python3.8/runpy.py", line 194, in _run_module_as_main return _run_code(code, main_globals, None, File "/usr/local/lib/python3.8/runpy.py", line 87, in _run_code exec(code, run_globals) File "/root/oktoberfest/__main__.py", line 8, in <module> main() File "/root/oktoberfest/oktoberfest.py", line 35, in main run_oktoberfest(args.search_dir, args.config_path) File "/root/oktoberfest/oktoberfest.py", line 160, in run_oktoberfest generate_spectral_lib(search_dir, config_path) File "/root/oktoberfest/oktoberfest.py", line 104, in generate_spectral_lib grpc_output_sec = spec_library.grpc_predict(spectra_div) File "/root/oktoberfest/spectral_library.py", line 107, in grpc_predict return predictions UnboundLocalError: local variable 'predictions' referenced before assignment make: *** [/oktoberfest/Makefile:23: run_oktoberfest] Error 2

WassimG commented 2 years ago

Hey Kevin,

it was a bug on our site, now both of your tasks are done as well.

yangkl96 commented 2 years ago

Just downloaded and they look good. Thank you