FW: MaAsLin question

[Levesque, Nicole M.]

Good afternoon – forwarding in case anyone hasn’t seen this yet.

Thanks,

Nicole

 

From: Arbeeva, Liubov <liubov_...@med.unc.edu>
Sent: Monday, November 04, 2019 8:36 AM
To: Huttenhower, Curtis <chut...@hsph.harvard.edu>; Levesque, Nicole M. <leve...@hsph.harvard.edu>
Subject: MaAsLin question

 

Dear all,

 

I am trying to run MaAsLin for sensitivity analysis (reviewer’s request).

My data is in QIIME format (version 1.9).

I tried to convert the data using your python program, but had an error:

 

.mapping.txt < otu_table.tsv > maaslin_input.pcl

  File “/apps/python/3.5.1/lib/python3.5/site.py", line 176

    file=sys.stderr)

        ^

SyntaxError: invalid syntax

 

I have python 3.5. I believe there is something wrong with sity.py library.

Just wanted to ask whether other users had similar issue before I contact our IT person to deal with python libraries.

 

Thank you in advance for your help.

 

Liubov Arbeeva

 

 

[Lauren McIver]

Hello Liubov, If you use python 2.7 it should resolve the error you are seeing. It looks like that utility script included with MaAsLin is not python 3 compatible.

Thanks,

Lauren

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