error message: Unknown Element in string: {sequence}. Found Elements: {x}") NameError: name 'x' is not defined make #48
Comments
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Hi, the x is a bug that will be resolved as soon as the newest version of Prosit goes online. Until then you can give me your Task id and i can check what Amino acid encodings we do not support. Some candidates that appear frequently are 'U' 'O' or any Modification encoding except M(ox). |
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Any thoughts on the above? Also, would you have a general ETA for new version? |
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Some sequences in your files seem to be replaced with numbers. Regarding the ETA is hard for me to say. @tkschmidt can you give a general ETA when the new Prosit version will become public? |
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Thanks @LLautenbacher . You were correct. I have since fixed the issue and am running 4 searches of around ~45MB each, but they've been running now for ~9 hours and counting. Not sure if that's normal? [](https://www.proteomicsdb.org/prosit/task/ABAE04B6AA02D7EB793317F0765998BB @tkschmidt Any thoughts on when the new version might be available either as downloadable source code or as a publicly accessible web-based system (such as the current prosit website)? |
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Are you sure these are the correct Task-IDs? They seem to have been uploaded ~4 hours before your comment. Regardless of this the tasks you sent are not started yet because the server is currently occupied with other jobs. |
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@LLautenbacher You may be correct again. They may have only been uploaded ~4 hours before my comment. That said, as of 6 am EST today, they're still processing, so I'm guessing it's because the server is currently occupied with other jobs. I'll check again tonight. Many thanks in advance for your assistance. |
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The prediction seems to have completed successfully! Thanks! @LLautenbacher If you have any thoughts regarding ETA, please feel free to let us know :) (even if it's something like "not before x years" etc :) |
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Reporting this issue on my end. See attached. |
I'm submitting a small csv file (~1 MB) but I'm getting this error message. I can't make sense of what seems to be the problem. I searched my input file, and I don't have any sequence with "x" in it.
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 <module> 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 123, in predict self.input.prepare_input(disable_progress_bar) File "/root/.pyenv/versions/3.6.0/src/prosit-grpc/prosit_grpc/inputPROSIT.py", line 15, in prepare_input self.sequences.prepare_sequences(flag_disable_progress_bar) File "/root/.pyenv/versions/3.6.0/src/prosit-grpc/prosit_grpc/inputPROSIT.py", line 143, in prepare_sequences self.character_to_array(flag_disable_progress_bar) File "/root/.pyenv/versions/3.6.0/src/prosit-grpc/prosit_grpc/inputPROSIT.py", line 118, in character_to_array total=len(self.character)): 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/__utils__.py", line 88, in split_modstring raise ValueError(f"Unknown Element in string: {sequence}. Found Elements: {x}") NameError: name 'x' is not defined make: *** [grpc_predict] Error 8The text was updated successfully, but these errors were encountered: