Hmp_client to download data - ftp error


#1

Please use this template to help us fix your problem quickly! Please don’t include sensitive information (including IP addresses) and fill in sections as appropriate.

CLIMB SERVICE PROBLEMS (Bryn, OpenStack, Launching VMs, Creating and attaching Volumes, etc.)

1. Describe the problem. Are there any error messages you can paste? Can you provide a screenshot of the problem (with sensitive information removed)?

2. What is the name of the VM or volume that the problem is affecting?

3. Where is the VM or volume hosted; Birmingham, Cardiff, Swansea or Warwick?

4. Is there any other information that you think might be helpful?

SOFTWARE OR APPLICATION PROBLEMS (Python can’t find the modules I installed, Prokka doesn’t predict any ORFs, etc.)

1. Describe the problem. Include links to any guides that you might be following and a brief history of the commands that you’ve run. Paste any error messages in code-blocks (paste, highlight and press Ctrl+Shift+C).

I’m trying to download microbiome data from HMP using the hmp client (https://github.com/ihmpdcc/hmp_client)

I run the following commands (after changing docker in /etc/group to include ubuntu as described in another thread):

git clone https://github.com/IGS/Chiron.git

Seems to install ok

Then run the following to launch (again, works fine):

./bin/hmp_client_interactive

Run the test file:

hmp_client opt/hmp_client/test/hmp_cart_example.tsv

Here it fails with the following error:

File "/usr/local/bin/hmp_client", line 13, in <module>
    from process_manifest import download_manifest
  File "/opt/hmp_client/hmp_client-1.2/bin/process_manifest.py", line 19, in <module>
    ftp.login('client') # any PW works as it's public
  File "/usr/lib/python3.5/ftplib.py", line 417, in login
    resp = self.sendcmd('USER ' + user)
  File "/usr/lib/python3.5/ftplib.py", line 272, in sendcmd
    return self.getresp()
  File "/usr/lib/python3.5/ftplib.py", line 243, in getresp
    raise error_temp(resp)
ftplib.error_temp: 421 Timeout

2. What operating system are you running; GVL, Ubuntu 16.04, Centos 7, etc.?

This is a standard GVL at Bham.

3. Is there any other information that you think might be helpful?


#2

Have you installed the dependencies listed here - https://github.com/IGS/Chiron.

The error you have encountered seems to be an generated by server. The server drop will drop connection if there are not any downloads/uploads of files.

I would contact the developers of the software with this query as they will have more detailed insight into how to deal with it.

I hope that helps,
Sion


#3

Thanks Sion, will do.
David


#4

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