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

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

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

Pat

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

Can you post the output of running…

system(ls)
system(pwd)

Thanks,
Pat

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

Sorry one more -

system(ls processed_data)

Pat

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

thnks!
SG

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)