Error running on MAC 64bit

[caroli...@gmail.com]

Hi!

I could run SDT on my laptop. Its a Mac 64bit.

I changed all inside 'bin' directory to executable files.

Here is the command:
python SDT_Mac64.py test.fas muscle

Here the error:

Loading sequences

Performing pairwise alignment: progress 2%Traceback (most recent call last):

  File "SDT_Mac64.py", line 148, in <module>

    Align_Wait(name_in,name_out,alg)                      #calling muscle

  File "SDT_Mac64.py", line 57, in Align_Wait

    proc=Popen(cmd,stdout=PIPE,stderr=PIPE)

  File "/usr/local/Cellar/python@2/2.7.17/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 394, in __init__

    errread, errwrite)

  File "/usr/local/Cellar/python@2/2.7.17/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1047, in _execute_child

    raise child_exception

OSError: [Errno 1] Operation not permitted


Someone can help me, please?

[Brejnev Muhire]

It seems python is not able to run the alignment via muscle.

To fix this, I would start by checking whether muscle can run in the terminal.

muscle3.8.31_i86darwin64 -in input.fas -out output.fas

If this is producing an alignment, then the problem would be with the subprocess module. 

Please email me on mubr...@gmail.com , so that I can help with extra steps for debugging.

Thanks

Brej

[bruno_...@hotmail.com]

Hi,
I'm having exactly the same problem in MAC 64 bit.
Did you guys find a solution?
Thanks

[Brejnev Muhire]

Hi SDT seems to have issues on mac:

Make sure you run it with python2.7

Some programs use do not still run on current versions of MAC, eg "neigbor" for phylogenetics tree

I get time to fix the issues.

However currently the Linux version works fine. It should be run with python2.7 as follows:

python2.7 SDT_Linux64.py test.fas muscle

here is the code on github:

https://github.com/brejnev/SDT-python