Hi, I'm trying to filter and plot genes in a given assembly however I keep getting this error: INFO:pyensembl.download_cache:Fetching /home/ekilinc/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.97.gtf.gz from URL https://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz
INFO:datacache.download:Downloading https://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz to /home/ekilinc/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.97.gtf.gz
Traceback (most recent call last):
File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connection.py", line 203, in _new_conn
sock = connection.create_connection(
File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/util/connection.py", line 85, in create_connection
raise err
File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
TimeoutError: [Errno 110] Connection timed out
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connectionpool.py", line 790, in urlopen
response = self._make_request(
File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connectionpool.py", line 491, in _make_request
raise new_e
File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connectionpool.py", line 467, in _make_request
self._validate_conn(conn)
File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connectionpool.py", line 1096, in _validate_conn
conn.connect()
File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connection.py", line 611, in connect
self.sock = sock = self._new_conn()
File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connection.py", line 212, in _new_conn
raise ConnectTimeoutError(
urllib3.exceptions.ConnectTimeoutError: (<urllib3.connection.HTTPSConnection object at 0x2aab23c6dab0>, 'Connection to ftp.ensembl.org timed out. (connect timeout=3600)')
The above exception was the direct cause of the following exception:
I tried to manually download and upload them in the given directory but it keeps asking for more files and it started to become overwhelming. Our server is an offline server, I was wondering if you have the list off, or a collection of all the required cache files for this command. Thanks a lot.
Hi, I'm trying to filter and plot genes in a given assembly however I keep getting this error: INFO:pyensembl.download_cache:Fetching /home/ekilinc/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.97.gtf.gz from URL https://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz INFO:datacache.download:Downloading https://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz to /home/ekilinc/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.97.gtf.gz Traceback (most recent call last): File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connection.py", line 203, in _new_conn sock = connection.create_connection( File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/util/connection.py", line 85, in create_connection raise err File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/util/connection.py", line 73, in create_connection sock.connect(sa) TimeoutError: [Errno 110] Connection timed out
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connectionpool.py", line 790, in urlopen response = self._make_request( File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connectionpool.py", line 491, in _make_request raise new_e File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connectionpool.py", line 467, in _make_request self._validate_conn(conn) File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connectionpool.py", line 1096, in _validate_conn conn.connect() File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connection.py", line 611, in connect self.sock = sock = self._new_conn() File "/rsrch5/home/neuro_rsrch/ekilinc/miniforge3/envs/neoloop/lib/python3.10/site-packages/urllib3/connection.py", line 212, in _new_conn raise ConnectTimeoutError( urllib3.exceptions.ConnectTimeoutError: (<urllib3.connection.HTTPSConnection object at 0x2aab23c6dab0>, 'Connection to ftp.ensembl.org timed out. (connect timeout=3600)')
The above exception was the direct cause of the following exception:
I tried to manually download and upload them in the given directory but it keeps asking for more files and it started to become overwhelming. Our server is an offline server, I was wondering if you have the list off, or a collection of all the required cache files for this command. Thanks a lot.