File "./phylophlan.py", line 393 except OSError, e:^ SyntaxError: invalid syn

[hilbert.h...@gmail.com]

Hello everyone,

I hope somebody can help me with this problem. I'm actually executing just "phylophlan.py -h" and I have no result show on the linux console.I have installed all dependencies without any problem. I just can see the following lines:

User@user:~/Phylophlan$ ./phylophlan.py -h

  File "./phylophlan.py", line 393
    except OSError, e:
                  ^
SyntaxError: invalid syntax

Thanks a lot,

Gil

[Francesco Asnicar]

Hello Gil,

Can you please verify which version of Python you have when executing "/usr/bin/env python"?

PhyloPhlAn works with Python2 and recent systems have Python3 as default.

In case this is not the problem causing the error, can you please provide the full output of PhyloPhlAn?

Many thanks,
Francesco

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[Konstantina Mitsi]

Hello!
I use pyenv to change among python versions. I have activated Python 2.7.17 but I am getting the same error. Any suggestions?
Thanks in advance.
Kons

El jueves, 28 de junio de 2018, 12:46:15 (UTC+2), francescoasnicar escribió:

Hello Gil,

Can you please verify which version of Python you have when executing "/usr/bin/env python"?

PhyloPhlAn works with Python2 and recent systems have Python3 as default.

In case this is not the problem causing the error, can you please provide the full output of PhyloPhlAn?

Many thanks,
Francesco

On Wed, Jun 27, 2018 at 5:33 PM <hilbert....@gmail.com> wrote:

Hello everyone,

I hope somebody can help me with this problem. I'm actually executing just "phylophlan.py -h" and I have no result show on the linux console.I have installed all dependencies without any problem. I just can see the following lines:

User@user:~/Phylophlan$ ./phylophlan.py -h

  File "./phylophlan.py", line 393
    except OSError, e:
                  ^
SyntaxError: invalid syntax

Thanks a lot,

Gil

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[Konstantina Mitsi]

So! Hello again!
Problem solved!
pyenv is not compatible with the ppa2 conda environment but it makes the trick for the bitbucket repository installation.
Cheers!
Kons