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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
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Error in online version #63

Closed bjgprt closed 3 years ago

bjgprt commented 3 years ago

In predicting Spectral Library, what is the limit of the csv file, please? I have tested with a file with 25 lines and it worked. However, when I tried larger files (>600000, less than 50M) it is always failed. Thanks!

Task AC6F33D04A4E553E95576D3D6DC9480D An error occured. Status code: 2 Error log keyboard_arrow_down WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. Traceback (most recent call last): File "oktoberfest/grpc_predict_peptidelist.py", line 36, in disable_progress_bar=True) File "/root/.pyenv/versions/3.6.0/src/prosit-grpc/prosit_grpc/predictPROSIT.py", line 153, in predict_to_hdf5 models=[irt_model, intensity_model]) File "/root/.pyenv/versions/3.6.0/src/prosit-grpc/prosit_grpc/predictPROSIT.py", line 133, in predict pred_object.predict(disable_progress_bar) File "/root/.pyenv/versions/3.6.0/src/prosit-grpc/prosit_grpc/PredObject.py", line 116, in predict disable_progress_bar=disable_progress_bar) File "/root/.pyenv/versions/3.6.0/src/prosit-grpc/prosit_grpc/PredObject.py", line 101, in send_requests total=n_batches): File "/root/.pyenv/versions/3.6.0/lib/python3.6/site-packages/tqdm/std.py", line 1107, in iter for obj in iterable: File "/root/.pyenv/versions/3.6.0/src/prosit-grpc/prosit_grpc/PredObject.py", line 66, in create_requests assert len(i) == len(j) TypeError: object of type 'NoneType' has no len() make: *** [grpc_predict] Error 8

LLautenbacher commented 3 years ago

Hi, your last entry is missing collision_energy and precursor_charge.