Does compleasm try to download something when run specifying lineage?

[olekto]

Hi, I am trying to get compleasm running, but run into an issue. Specifically, I get this error:

Traceback (most recent call last):
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/urllib/request.py", line 1350, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/http/client.py", line 1281, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/http/client.py", line 1327, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/http/client.py", line 1276, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/http/client.py", line 1036, in _send_output
    self.send(msg)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/http/client.py", line 976, in send
    self.connect()
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/http/client.py", line 1443, in connect
    super().connect()
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/http/client.py", line 948, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/socket.py", line 728, in create_connection
    raise err
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/socket.py", line 716, in create_connection
    sock.connect(sa)
TimeoutError: [Errno 110] Connection timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/bin/compleasm", line 10, in <module>
    sys.exit(main())
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/site-packages/compleasm.py", line 2534, in main
    args.func(args)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/site-packages/compleasm.py", line 2425, in run
    mode=mode)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/site-packages/compleasm.py", line 2092, in __init__
    self.downloader = Downloader(library_path)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/site-packages/compleasm.py", line 85, in __init__
    self.lineage_description, self.placement_description = self.download_file_version_document()
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/site-packages/compleasm.py", line 127, in download_file_version_document
    urllib.request.urlretrieve(hash_url, hash_download_path)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/urllib/request.py", line 247, in urlretrieve
    with contextlib.closing(urlopen(url, data)) as fp:
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/urllib/request.py", line 222, in urlopen
    return opener.open(url, data, timeout)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/urllib/request.py", line 525, in open
    response = self._open(req, data)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/urllib/request.py", line 543, in _open
    '_open', req)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/urllib/request.py", line 503, in _call_chain
    result = func(*args)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/urllib/request.py", line 1393, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/cluster/projects/nn8013k/programs/miniconda3/envs/compleasm/lib/python3.7/urllib/request.py", line 1352, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 110] Connection timed out>

The command is this: compleasm run -a default_filt.hic.hap1.p_ctg.fa -l aves -L /cluster/projects/nn8013k/opt/busco_dbs/lineages/ -t 10 -o compleasm_test

When running on the login nodes, it looks like it actually downloads aves and eukaryota, even though the folders existed in /cluster/projects/nn8013k/opt/busco_dbs/lineages/.

Am I doing something wrong?

Our computing nodes do not have internet access, and I don't think it is nice practice to download something without letting the user know that it is happening. How can I turn this off? That is, can I download something before submitting the job to the cluster?

Thank you.

Ole