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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
630 stars 292 forks source link

What is it downloading? #1391

Closed andersonwinkler closed 5 years ago

andersonwinkler commented 5 years ago

And why does it need to download things if the machine has no internet access?

cat ap2_13392997_97.e
/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8
  warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning)
/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8
  warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning)
Download failed, retrying (attempt 1)
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Process Process-2:
Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 704, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/multiprocessing/process.py", line 93, in run
    self._target(*self._args, **self._kwargs)
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/fmriprep/cli/run.py", line 553, in build_workflow
    ignore_aroma_err=opts.ignore_aroma_denoising_errors,
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 211, in init_fmriprep_wf
    ignore_aroma_err=ignore_aroma_err,
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 447, in init_single_subject_wf
    num_t1w=len(subject_data['t1w']))
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/fmriprep/workflows/anatomical.py", line 240, in init_anat_preproc_wf
    omp_nthreads=omp_nthreads)
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/fmriprep/workflows/anatomical.py", line 625, in init_skullstrip_ants_wf
    template_dir = get_template(template_name)
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/getters.py", line 72, in get_template
    url=url, resume=resume, verbose=verbose)
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/getters.py", line 61, in get_dataset
    filetype='tar', resume=resume, verbose=verbose, md5sum=md5)
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 156, in fetch_file
    verbose=verbose, retry=retry + 1)
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 156, in fetch_file
    verbose=verbose, retry=retry + 1)
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 156, in fetch_file
    verbose=verbose, retry=retry + 1)
  [Previous line repeated 16 more times]
  File "/gpfs/gsfs6/users/EDB/AP2+rest/code/env-hpc/lib/python3.6/site-packages/niworkflows/data/utils.py", line 146, in fetch_file
    data = urlopen(request)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>
effigies commented 5 years ago

Templates for skull-stripping and normalization. These are included in the Docker image published to DockerHub:

https://github.com/poldracklab/fmriprep/blob/6d7bc7568ced4e5244b786138acf7863b498f814/Dockerfile#L147-L153

You can follow these lines to pre-download and prepare your environment, i.e. set CRN_SHARED_DATA in your shell configurations and run tools/get_templates.sh. Note that this has changed in version 1.2.2, so you should run the get_templates.sh script from the release version you're using.

As an aside, if you have no internet connection, you should also use the --notrack command-line argument to avoid fMRIPrep trying to send back usage statistics. It will do no harm, but it will put some ugly exceptions in your output.

andersonwinkler commented 5 years ago

Great, thanks Chris! It went past that point, and it seems to be running fine. Thanks! Cheers, Anderson

effigies commented 5 years ago

Great! Please reopen if problems re-emerge.