Open gabridinosauro opened 2 years ago
Hi Gabri!
I have the same issue :( Did you find the solution?
Thanks, Ilaria
Hello all,
No solution yet to this day. How about you, Ilaira?
Gabri
Noone, It wold be very cool to have this tool functioning!
Hi @mrgambero and @Hela06, I've been working on a fix to this issue. I believe it's actually an issue with KEGG_parser, rather than AMON itself. Sorry about the delay on this, but I'll keep you posted on progress!
Hello @sterrettJD thanks a lot! Yes keep me posted please!
Gabri
Hi everyone,
Still no AMON :(. Anyone with any news?
Gabri
Hey @mrgambero, good news! We think we have the issue in KEGG-Parser
that was causing this patched, and I just pushed the new version to PyPI.
Could you run pip install --upgrade KEGG-Parser
in your conda environment that you're using for AMON, and then try to run AMON again? This should fix the ValueError: What is SYMBOL in ...
(I hope).
Please let me know if upgrading KEGG-Parser to 0.0.5 fixes things!
Hello @sterrettJD ,
I am sorry I have not had the chance to try it again, bit busy with other projects atm but I will try as soon as I will restart working on it. Sorry!
Gabri
Hello, sorry for the delay. I now get this error: amon.py -o /Users/gabri/Library/CloudStorage/Box-Box/CPAE_manuscript/metabolites/AMON -i /Users/gabri/Library/CloudStorage/Box-Box/CPAE_manuscript/metabolites/ko_list_metagen.txt --other_gene_set /Users/gabri/Library/CloudStorage/Box-Box/CPAE_manuscript/metabolites/Ko_Human.txt Traceback (most recent call last): File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/site-packages/aiohttp/connector.py", line 980, in _wrap_create_connection return await self._loop.create_connection(*args, **kwargs) # type: ignore[return-value] # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/asyncio/base_events.py", line 1085, in create_connection raise exceptions[0] File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/asyncio/base_events.py", line 1069, in create_connection sock = await self._connect_sock( ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/asyncio/base_events.py", line 973, in _connect_sock await self.sock_connect(sock, address) File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/asyncio/selector_events.py", line 634, in sock_connect return await fut ^^^^^^^^^ File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/asyncio/selector_events.py", line 674, in _sock_connect_cb raise OSError(err, f'Connect call failed {address}') TimeoutError: [Errno 60] Connect call failed ('133.103.200.27', 80)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/gabri/mambaforge/envs/AMON/bin/amon.py", line 74, in
Hello, Thanks for your work.
I am trying to tun AMON but I do not seem to be able to get any results out.
Specifically, I always encounter this problem: amon.py -i Komicro.txt -o output_AMON --detected_compounds COlist1.txt --other_gene_set mus_mucus1.txt Traceback (most recent call last): File "/Users/gabri/opt/miniconda3/envs/AMON/bin/amon.py", line 74, in
main(kos_loc, output_dir, other_kos_loc, detected_compounds, name1, name2, keep_separated, samples_are_columns,
File "/Users/gabri/opt/miniconda3/envs/AMON/lib/python3.10/site-packages/AMON/predict_metabolites.py", line 283, in main
ko_dict = get_kegg_record_dict(set(all_kos), parse_ko, ko_file_loc)
File "/Users/gabri/opt/miniconda3/envs/AMON/lib/python3.10/site-packages/KEGG_parser/downloader.py", line 55, in get_kegg_record_dict
records = get_from_kegg_api(loop, list_of_ids, parser)
File "/Users/gabri/opt/miniconda3/envs/AMON/lib/python3.10/site-packages/KEGG_parser/downloader.py", line 49, in get_from_kegg_api
return [parser(raw_record) for raw_record in loop.run_until_complete(kegg_download_manager(loop, list_of_ids))]
File "/Users/gabri/opt/miniconda3/envs/AMON/lib/python3.10/site-packages/KEGG_parser/downloader.py", line 49, in
return [parser(raw_record) for raw_record in loop.run_until_complete(kegg_download_manager(loop, list_of_ids))]
File "/Users/gabri/opt/miniconda3/envs/AMON/lib/python3.10/site-packages/KEGG_parser/parsers.py", line 195, in parse_ko
raise ValueError('What is {} in {}?'.format(current_entry_name, ko_dict['ENTRY']))
ValueError: What is SYMBOL in K09637?
Any idea of why this is happening?
Thanks in advance! Gabri