NameError: name 'init' is not defined

[Hila Korach - Rechtman]

Hi LEfSe users!

since LEfSe sever is making problems recently, i tried to use the VM and the run_lefse.py command. 

i started with:

format_input.py ko_L3.txt ko_L3.lefse

and than:

run_lefse.py ko_L3.lefse ko_L3.lefse.out

which gave me this error:

Traceback (most recent call last):

  File "//lefse/run_lefse.py", line 56, in <module>

    init()

NameError: name 'init' is not defined

i will appreciate any insights on how to fix it...

cheers, 

Hila

[Hila Korach - Rechtman]

can anyone please help?

thanks so much!

בתאריך יום שלישי, 21 בנובמבר 2017 בשעה 13:28:28 UTC+2, מאת Hila Korach - Rechtman:

[jfg]

Heya Hila, 

   I spy picrust data! ;) If you haven't fixed this, I think this is because you're not telling LEfSe to use python2.7 (which it needs, as it won't run on python3+). 

   If this is the case, theres an easy fix: try putting "python2.7" at the beginning of each call:

python2.7 format_input.py ko_L3.txt ko_L3.lefse

python2.7 run_lefse.py ko_L3.lefse ko_L3.lefse.out

and so on!

all the best

jfg

[Hila Korach - Rechtman]

thanks for your answer!

however, when i added the python2.7 on the first command (format_input.py) it got this error:

python2.7: can't open file 'format_input.py': [Errno 2] No such file or directory

when i delete the "python2.7", the format_input.py worked ok, but got the same error for the second command (run_lefse.py):

python2.7: can't open file 'run_lefse.py': [Errno 2] No such file or directory

i did it with and without adding the "python2.7" addition (for the second command).

your help is very much appreciated! 

Hila

בתאריך יום שלישי, 28 בנובמבר 2017 בשעה 14:54:34 UTC+2, מאת jfg:

[Leah Reshef]

Which VM are you using ? If its docker than you dont need to specify the python 2.7. Sounds to me like something in your input data is off; download teh lefse example input file , is that running OK? If so you can attcah your input file here and we'll see if we can spot the problem

[brett...@gmail.com]

Hello,

I am having a similar problem using Docker. Why I try to use the command "format_input.py" I get the response "IOError: [Errno 2] No such file or directory: "

When I tried the example input file, I got the same error. 

Any ideas how to fix this?

Thanks,

Brett

[brett...@gmail.com]

Also, I'm using Mac with OS X El Capitan 10.11.6, if that helps.

Brett

[Leah Reshef]

Hi Bret, can you see your input file if you run 'ls' ? Could be the directory is not mounting properly.