Lefse [ERROR]: requesting groups not present in files, aborting. Segmentation fault: 11

1

Hi!
I’m trying to run lefse according to Riffomonas tutorials on youtube, but this error appears:
[ERROR]: requesting groups not present in files, aborting.
Segmentation fault: 11.

what am I doing wrong?
Thnks so much!
SG

2

Can you post the syntax of the command you are running along with what your design file looks like?

Pat

3

the syntax of the command i’m running is:
mothur > lefse(shared=sano_diarrea.shared, design=sano_diarrea.design, inputdir=processed_data)

this is what appears:
[ERROR]: cannot access processed_data/

Unable to open sano_diarrea.shared. Trying MOTHUR_FILES directory /Users/sergiogeorge 1/Desktop/code_club/mothur/sano_diarrea.shared.

Unable to open sano_diarrea.design. Trying MOTHUR_FILES directory /Users/sergiogeorge 1/Desktop/code_club/mothur/sano_diarrea.design.

You did not provide a class, using grupo.

Comparing Sano-Diarrea:

[ERROR]: requesting groups not present in files, aborting.

Segmentation fault: 11

logout

Saving session…

…copying shared history…

…saving history…truncating history files…

…completed.

[Proceso completado]

The design file looks like this:
A tibble: 83 × 2
Group grupo

1 sample1 Sano
2 sample10 Diarrea
3 sample11 Diarrea
4 sample12 Diarrea
5 sample13 Sano
6 sample14 Diarrea
7 sample15 Diarrea
8 sample16 Diarrea
9 sample17 Sano
10 sample18 Diarrea

… with 73 more rows

4

Can you post the output of running…

system(ls)
system(pwd)

Thanks,
Pat

5

mothur > system(ls)
GENUS BARRCHART AND HEATMAP.R
GENUS LOGSCALE.R
GENUS STATISTICS GRAPHS.R
GENUS STATISTICS.R
GENUS box plot and range plot.R
Genus grouped barchart 3 groups.R
Grouped box plot and range plot.R
Grouped plott of jittered data Phylum.R
Grouped stacked barchart Phyllum.R
HEATMAP MICROBIOTA SERGIO .R
LDA Genus 3 grupos.R
MICROBIOTA SERGIO DEC22.R
MICROBIOTA SERGIO GRAFICO BARRA PHYLLUM 3 GRUPOS.R
PHYLUM STATISTICS GRAPHS.R
code_club.Rproj
mothur
mothur.1672760890.logfile
mothur.1672777717.logfile
mothur.1672777838.logfile
mothur.1672779425.logfile
mothur.1673372894.logfile
mothur.1673373008.logfile
processed_data
raw_data
schubert.subsample.shared

mothur > system(pwd)
/Users/sergiogeorge 1/Desktop/code_club

Thanks!! SG

6

Sorry one more -

system(ls processed_data)

Pat

7

mothur > system(ls processed_data)
sano_diarrea.design
sano_diarrea.shared
sano_diarrea2.design
sano_diarrea2.shared

thnks!
SG

8

Sorry, but I’m really not sure what’s going on. I wonder if you were in a different directory when you first ran the command and go the error. Could you try running this?

mothur > lefse(shared=processed_data/sano_diarrea.shared, design=processed_data/sano_diarrea.design)
9

I am having the same issue on Windows 10. I am using the most recent release version of Mothur.

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10

I followed the Code Club tutorial on youtube and adjusted the files accordingly. I just added the label and numOtus columns to the shared file and worked fine. Error was gone.

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