No such file or directory '/dev/null'

[Anh Nguyen]

Hi Nicola,

Thanks a lot for providing this software. 

I've encountered a problem while trying to build a new tree.

The error is reported as follows:

ret = sb.call([prog],stdout=open('/dev/null'),stderr=open('/dev/null'))

IOError: [Errno 2] No such file or directory '/dev/null'

This is related to the 3 external dependencies. I added the correct versions to ./phylophlan main folder, and named them 'muscle', 'usearch', and 'FastTree' as suggested.

I am not sure whether I have missed some steps, or there is a problem with the external softwares.

Could you please help me with this?

Thank you very much.

Anh

[Anh Nguyen]

After reading the bitbucket page, I realised it was a cross platform problem, as I'm using Windows. It's solved now. 

Thanks!

[Anh Nguyen]

Hi, I have another problem. With FastTree and others in the /phylophlan folder, phylophlan.py still can't seem to locate it even after I added the folder to system path. I'm running it on Windows. I'm really sorry for asking such a trivial question, but I have been trying to get the answer on the internet and couldn't find any useful information. Thank you so much!
Anh

[Francesco Asnicar]

Hi Anh,

First of all, thank you for using PhyloPhlAn.

We knew and fixed the "/dev/null" problem, even though the actual fix is not present in the main branch but in the dev branch. Soon we will merge the two branches applying several fixes to the main branch of PhyloPhlAn.

It is actually not needed to insert the programs in the PhyloPhlAn folder. The only things that you have to be sure are:

• that they are named: muscle, usearch, and FastTree (it seems so from your first email);
  
• they are present in the system path. You can type the command in the prompt and see if they were added or not.

Unfortunately I never tested PhyloPhlAn in the Windows environment, I think I'll give it a try in the next few days.

Let me know if the above points are working and PhyloPhlAn still doesn't run.

Thanks,

Francesco Asnicar

e-mail | WebSite

On Tue, Feb 3, 2015 at 2:24 AM, Anh Nguyen <nguyent...@gmail.com> wrote:

Hi, I have another problem. With FastTree and others in the /phylophlan folder, phylophlan.py still can't seem to locate it even after I added the folder to system path. I'm running it on Windows. I'm really sorry for asking such a trivial question, but I have been trying to get the answer on the internet and couldn't find any useful information. Thank you so much!
Anh

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[Anh Nguyen]

Thanks, Francesco, for the prompt reply.

I tried again, this time setting the path directly from the command prompt before running phylophlan and it seems to be working.

Thanks, again.

Anh