Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

no valid URL in the manifest file #24

Open
eggomez opened this issue May 17, 2023 · 1 comment
Open

no valid URL in the manifest file #24

eggomez opened this issue May 17, 2023 · 1 comment
Assignees
@JPReceveur

Comments

@eggomez
Copy link

eggomez commented May 17, 2023

Hi there, trying to download these datafiles: https://assets.nemoarchive.org/dat-zkgd0it

I add files to my cart, download the manifest file, installed portal_client but get the error "no valid URL in the manifest file" (full error with --debug below.

Any alternative way to download these data?

Thanks!
Elaine

(base) eg197@dcc-login-02 /hpc/group/guevaralab/sc-data/existing-data/Ma_data $ portal_client --manifest NeMO_manifest_2b107849a.tsv --destination ./chimpanzee/ --debug
2023-05-17 17:03:53,794 - root - DEBUG - In validate_cli.
2023-05-17 17:03:53,794 - root - DEBUG - Creating ManifestProcessor.
2023-05-17 17:03:53,839 - boto - DEBUG - Retrieving credentials from metadata server.
2023-05-17 17:03:54,846 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:03:54,943 - boto - ERROR - Unable to read instance data, giving up
2023-05-17 17:03:54,943 - convert_to_manifest - DEBUG - In file_to_manifest.
2023-05-17 17:03:54,945 - convert_to_manifest - DEBUG - In tsv_to_manifest.
2023-05-17 17:03:54,947 - root - DEBUG - About to start downloading manifest.
2023-05-17 17:03:54,947 - manifest_processor.ManifestProcessor - DEBUG - In download_manifest.
2023-05-17 17:03:54,947 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:03:55,448 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:03:55,449 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB2169_4_S1_L001-001.fastq.tar
2023-05-17 17:03:55,449 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:03:55,951 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:03:55,951 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB2169_3_S1_L001-001.fastq.tar
2023-05-17 17:03:55,951 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:03:56,453 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:03:56,453 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB1841_4_S1_L001-001.fastq.tar
2023-05-17 17:03:56,453 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:03:56,955 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:03:56,955 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB166_4_S1_L001-001.fastq.tar
2023-05-17 17:03:56,956 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:03:57,457 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:03:57,458 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB1841_1_S1_L001-001.fastq.tar
2023-05-17 17:03:57,458 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:03:57,959 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:03:57,960 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB166_2_S1_L001-001.fastq.tar
2023-05-17 17:03:57,960 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:03:58,462 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:03:58,462 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB1841_2_S1_L001-001.fastq.tar
2023-05-17 17:03:58,462 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:03:58,964 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:03:58,964 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB2169_1_S1_L001-001.fastq.tar
2023-05-17 17:03:58,964 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:03:59,466 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:03:59,467 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB165_4_S1_L001-001.fastq.tar
2023-05-17 17:03:59,467 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:03:59,968 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:03:59,970 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB2169_2_S1_L001-001.fastq.tar
2023-05-17 17:03:59,970 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:04:00,472 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:04:00,473 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB166_3_S1_L001-001.fastq.tar
2023-05-17 17:04:00,473 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:04:00,974 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:04:00,974 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB165_3_S1_L001-001.fastq.tar
2023-05-17 17:04:00,975 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:04:01,476 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:04:01,477 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB165_2_S1_L001-001.fastq.tar
2023-05-17 17:04:01,477 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:04:01,978 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:04:01,978 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB1841_3_S1_L001-001.fastq.tar
2023-05-17 17:04:01,979 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:04:02,480 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:04:02,481 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB166_1_S1_L001-001.fastq.tar
2023-05-17 17:04:02,481 - manifest_processor.ManifestProcessor - DEBUG - In _get_prioritized_endpoint.
2023-05-17 17:04:02,982 - boto - ERROR - Caught exception reading instance data
Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/hpc/home/eg197/miniconda3/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/hpc/home/eg197/miniconda3/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/hpc/home/eg197/miniconda3/lib/python3.7/site-packages/boto-2.49.0-py3.7.egg/boto/utils.py", line 217, in retry_url
r = opener.open(req, timeout=timeout)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/hpc/home/eg197/miniconda3/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError:
2023-05-17 17:04:02,983 - boto - ERROR - Unable to read instance data, giving up
No valid URL found in the manifest for file ID PTB165_1_S1_L001-001.fastq.tar

Not all files (total of 16) were downloaded successfully. Number of failures:
16 -- no valid URL in the manifest file
0 -- URL is present in manifest, but not accessible at the location specified
0 -- MD5 checksum failed for file (file is corrupted or the wrong MD5 is associated)
@nsuvarnaiari
Copy link

Hi @eggomez

Sorry for the inconvenience. Please visit the link below to download the open access files:
https://data.nemoarchive.org/biccn/grant/u01_sestan/sestan/transcriptome/sncell/10x_v3/

Thanks,
Suvvi

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@JPReceveur JPReceveur

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@nsuvarnaiari @eggomez @JPReceveur