database downloading fails

[ye00ye]

asking for help, I met problem when trying to download database

[02/26/2023 11:59:04 PM] INFO: Command: Download database. Checking internal path information.
Traceback (most recent call last):
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/urllib3/connection.py", line 174, in _new_conn
conn = connection.create_connection(
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/urllib3/util/connection.py", line 95, in create_connection
raise err
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/urllib3/util/connection.py", line 85, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/urllib3/connectionpool.py", line 703, in urlopen
httplib_response = self._make_request(
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/urllib3/connectionpool.py", line 386, in _make_request
self._validate_conn(conn)
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/urllib3/connectionpool.py", line 1042, in _validate_conn
conn.connect()
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/urllib3/connection.py", line 358, in connect
self.sock = conn = self._new_conn()
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/urllib3/connection.py", line 186, in _new_conn
raise NewConnectionError(
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f1ab1046e50>: Failed to establish a new connection: [Errno 111] Connection refused

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/requests/adapters.py", line 489, in send
resp = conn.urlopen(
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/urllib3/connectionpool.py", line 787, in urlopen
retries = retries.increment(
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/urllib3/util/retry.py", line 592, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='zenodo.org', port=443): Max retries exceeded with url: /record/5571251 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f1ab1046e50>: Failed to establish a new connection: [Errno 111] Connection refused'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/yanjiuyuan/Project/huangqiang/checkm2/bin/../checkm2/zenodo_backpack.py", line 164, in _retrieve_record_ID
r = requests.get(DOI, timeout=15.)
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/requests/sessions.py", line 587, in request
resp = self.send(prep, **send_kwargs)
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/requests/sessions.py", line 723, in send
history = [resp for resp in gen]
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/requests/sessions.py", line 723, in
history = [resp for resp in gen]
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/requests/sessions.py", line 266, in resolve_redirects
resp = self.send(
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/requests/sessions.py", line 701, in send
r = adapter.send(request, **kwargs)
File "/yanjiuyuan/userLogin/huangqiang/miniconda3/envs/checkm2/lib/python3.8/site-packages/requests/adapters.py", line 565, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='zenodo.org', port=443): Max retries exceeded with url: /record/5571251 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f1ab1046e50>: Failed to establish a new connection: [Errno 111] Connection refused'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "bin/checkm2", line 280, in
fileManager.DiamondDB().download_database(args.path)
File "/yanjiuyuan/Project/huangqiang/checkm2/bin/../checkm2/fileManager.py", line 127, in download_database
backpack_downloader.download_and_extract(download_location, DOI, progress_bar=True, no_check_version=False)
File "/yanjiuyuan/Project/huangqiang/checkm2/bin/../checkm2/zenodo_backpack.py", line 46, in download_and_extract
recordID = self._retrieve_record_ID(DOI)
File "/yanjiuyuan/Project/huangqiang/checkm2/bin/../checkm2/zenodo_backpack.py", line 166, in _retrieve_record_ID
raise ZenodoConnectionException('Connection error: {}'.format(e))
checkm2.zenodo_backpack.ZenodoConnectionException: Connection error: HTTPSConnectionPool(host='zenodo.org', port=443): Max retries exceeded with url: /record/5571251 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f1ab1046e50>: Failed to establish a new connection: [Errno 111] Connection refused'))

[chklovski]

Hi,

It looks like you are failing to establish a connection to Zenodo (where the database is hosted) for some reason. You can try manually downloading the current database at: https://zenodo.org/record/5571251/files/checkm2_database.tar.gz and then point checkm2 to is using checkm2 database --setdblocation /path/to/downloaded_database.dmnd

[ye00ye]

thanks for your help, i will try | | ye--ye | | ***@***.*** | ---- Replied Message ---- | From | Alex ***@***.***> | | Date | 2/27/2023 22:22 | | To | ***@***.***> | | Cc | ***@***.***> , ***@***.***> | | Subject | Re: [chklovski/CheckM2] database downloading fails (Issue #50) | Hi, It looks like you are failing to establish a connection to Zenodo (where the database is hosted) for some reason. You can try manually downloading the current database at: https://zenodo.org/record/5571251/files/checkm2_database.tar.gz and then point checkm2 to is using checkm2 database --setdblocation /path/to/downloaded_database.dmnd — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[chklovski]

Closed due to inactivity. Feel free to reopen if problem persists.