can't run LEfSe with HUMAnN output via Galaxy

[mark....@tgac.ac.uk]

Hi,

I'm running v 0.99 and don't see a *-lefse.txt as output.

After looking at other posts here, I tried formatting my '04b-hit-keg-mpm-cop-nul-nve-nve.txt' HUMAnN output [as per https://bitbucket.org/biobakery/biobakery/wiki/humann#rst-header-using-lefse] for LEfSe analysis via the Galaxy server at http://huttenhower.sph.harvard.edu/galaxy/root/index

I loaded the data as 'tabular', and formatted the data for LEfSe OK. However, when I run the LDA step I see the errors below.

Is this a problem with my input file to start with or are there darker forces at work?

Thanks,

Mark

/bin/sh: line 1: 18775 Segmentation fault      (core dumped) python /home/usr/local/galaxy-dist/tools/lefse/run_lefse.py /home/usr/local/galaxy-dist/database/files/000/152/dataset_152552.dat /home/usr/local/galaxy-dist/database/files/000/152/dataset_152553.dat -l 0.1 -a 0.05 -w 0.05 -e 0 -y 0 -f 0.9

cannot find system Renviron

[Afrah Shafquat]

Hello Mark,

Can you please send me the formatted file that you are using as input for LEfSe?

This will allow me to understand the issue.

--Afrah

[mark alston (TGAC)]

Thank you for getting back to me.

I meant to say that when I tried again earlier this week the same file worked fine.

 

Best wishes,

Mark

[Shafquat, Afrah]

Hello Mark,

That sounds great. Please let me know if the issue arises again.

Sincerely,

Afrah Shafquat

Program Manager

The Huttenhower Lab

Department of Biostatistics

Harvard School of Public Health

On May 23, 2014, at 12:12 PM, mark alston (TGAC) <mark....@tgac.ac.uk> wrote:

Thank you for getting back to me.

I meant to say that when I tried again earlier this week the same file worked fine.

 

Best wishes,

Mark

 

From: humann...@googlegroups.com [mailto:humann-us...@googlegroups.com] On Behalf Of Afrah Shafquat
Sent: 23 May 2014 16:48
To: humann...@googlegroups.com
Subject: Re: can't run LEfSe with HUMAnN output via Galaxy

 

Hello Mark,

Can you please send me the formatted file that you are using as input for LEfSe?

This will allow me to understand the issue.

 

--Afrah

On Friday, May 16, 2014 6:58:08 AM UTC-4,mark....@tgac.ac.uk wrote:

Hi,

I'm running v 0.99 and don't see a *-lefse.txt as output.

After looking at other posts here, I tried formatting my '04b-hit-keg-mpm-cop-nul-nve-nve.txt' HUMAnN output [as perhttps://bitbucket.org/biobakery/biobakery/wiki/humann#rst-header-using-lefse] for LEfSe analysis via the Galaxy server athttp://huttenhower.sph.harvard.edu/galaxy/root/index