Issue

[gabridinosauro]

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

[Hela06]

Hi Gabri!

I have the same issue :( Did you find the solution?

Thanks,
Ilaria

[gabridinosauro]

Hello all,

No solution yet to this day.
How about you, Ilaira?

Gabri

[gabridinosauro]

Noone, It wold be very cool to have this tool functioning!

[sterrettJD]

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!

[gabridinosauro]

Hello @sterrettJD thanks a lot! Yes keep me posted please!

Gabri

[gabridinosauro]

Hi everyone,

Still no AMON :(.
Anyone with any news?

Gabri

[sterrettJD]

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!

[gabridinosauro]

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

[gabridinosauro]

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
main(kos_loc, output_dir, other_kos_loc, detected_compounds, name1, name2, keep_separated, samples_are_columns,
File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/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/mambaforge/envs/AMON/lib/python3.11/site-packages/KEGG_parser/downloader.py", line 88, in get_kegg_record_dict
records = get_from_kegg_api(loop, list_of_ids, parser)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/site-packages/KEGG_parser/downloader.py", line 78, 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/mambaforge/envs/AMON/lib/python3.11/asyncio/base_events.py", line 653, in run_until_complete
return future.result()
^^^^^^^^^^^^^^^
File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/site-packages/KEGG_parser/downloader.py", line 47, in kegg_download_manager
results = await asyncio.gather(*tasks)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/site-packages/KEGG_parser/downloader.py", line 31, in download_coroutine
async with session.get(url) as response:
File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/site-packages/aiohttp/client.py", line 1141, in aenter
self._resp = await self._coro
^^^^^^^^^^^^^^^^
File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/site-packages/aiohttp/client.py", line 536, in _request
conn = await self._connector.connect(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/site-packages/aiohttp/connector.py", line 540, in connect
proto = await self._create_connection(req, traces, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/site-packages/aiohttp/connector.py", line 901, in _create_connection
_, proto = await self._create_direct_connection(req, traces, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/site-packages/aiohttp/connector.py", line 1209, in _create_direct_connection
raise last_exc
File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/site-packages/aiohttp/connector.py", line 1178, in _create_direct_connection
transp, proto = await self._wrap_create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gabri/mambaforge/envs/AMON/lib/python3.11/site-packages/aiohttp/connector.py", line 988, in _wrap_create_connection
raise client_error(req.connection_key, exc) from exc
aiohttp.client_exceptions.ClientConnectorError: Cannot connect to host rest.kegg.jp:80 ssl:default [Connect call failed ('133.103.200.27', 80)]