mothur

Make.lefse: query

Hi there!
what format does the .design file need to have to run make.lefse command? I’d be very grateful if somebody could give me an example to adjust it to my own data

Here you go… https://mothur.org/wiki/Design_File

Thanks! I had already noticed that and followed the same structure… but when I try to run the command I get the following error:

make.lefse(shared=CombinedV1V3.unique.good.filter.dgc.shared, constaxonomy=CombinedV1V3.unique.good.filter.dgc.0.03.cons.taxonomy, design=Experimental_design.design,groups=P1A10final.redundant.fasta-P1A11final.redundant.fasta-P1A12final.redundant.fasta-P1A1final.redundant.fasta-P1A2final.redundant.fasta-P1A3final.redundant.fasta-P1A4final.redundant.fasta-P1A5final.redundant.fasta-P1A6final.redundant.fasta-P1A7final.redundant.fasta-P1A8final.redundant.fasta-P1A9final.redundant.fasta-P1B10final.redundant.fasta-P1B11final.redundant.fasta-P1B12final.redundant.fasta-P1B1final.redundant.fasta-P1B2final.redundant.fasta-P1B3final.redundant.fasta-P1B4final.redundant.fasta-P1B5final.redundant.fasta-P1B6final.redundant.fasta-P1B7final.redundant.fasta-P1B8final.redundant.fasta-P1B9final.redundant.fasta-P1C10final.redundant.fasta-P1C11final.redundant.fasta-P1C12final.redundant.fasta-P1C1final.redundant.fasta-P1C2final.redundant.fasta-P1C3final.redundant.fasta-P1C4final.redundant.fasta-P1C5final.redundant.fasta-P1C6final.redundant.fasta-P1C7final.redundant.fasta-P1C8final.redundant.fasta-P1C9final.redundant.fasta-P1D10final.redundant.fasta-P1D11final.redundant.fasta-P1D12final.redundant.fasta-P1D1final.redundant.fasta-P1D2final.redundant.fasta-P1D3final.redundant.fasta-P1D4final.redundant.fasta-P1D5final.redundant.fasta-P1D6final.redundant.fasta-P1D7final.redundant.fasta-P1D8final.redundant.fasta-P1D9final.redundant.fasta-P1E10final.redundant.fasta-P1E11final.redundant.fasta-P1E12final.redundant.fasta-P1E1final.redundant.fasta-P1E2final.redundant.fasta-P1E3final.redundant.fasta-P1E4final.redundant.fasta-P1E5final.redundant.fasta-P1E6final.redundant.fasta-P1E7final.redundant.fasta-P1E8final.redundant.fasta-P1E9final.redundant.fasta- P1F1final.redundant.fasta-P1F2final.redundant.fasta-P1F3final.redundant.fasta-P1F4final.redundant.fasta-P1F5final.redundant.fasta-P1F6final.redundant.fasta- P1G10final.redundant.fasta-P1G11final.redundant.fasta-P1G12final.redundant.fasta-P1G3final.redundant.fasta-P1G4final.redundant.fasta-P1G5final.redundant.fasta-P1G6final.redundant.fasta-P1G7final.redundant.fasta-P1G8final.redundant.fasta-P1G9final.redundant.fasta-P1H10final.redundant.fasta-P1H11final.redundant.fasta-P1H12final.redundant.fasta-P1H1final.redundant.fasta-P1H2final.redundant.fasta-P1H3final.redundant.fasta-P1H4final.redundant.fasta-P1H5final.redundant.fasta-P1H6final.redundant.fasta-P1H7final.redundant.fasta-P1H8final.redundant.fasta-P1H9final.redundant.fasta-P2A10final.redundant.fasta-P2A11final.redundant.fasta-P2A12final.redundant.fasta-P2A1final.redundant.fasta-P2A2final.redundant.fasta-P2A3final.redundant.fasta-P2A4final.redundant.fasta-P2A5final.redundant.fasta-P2A6final.redundant.fasta-P2A7final.redundant.fasta-P2A8final.redundant.fasta-P2A9final.redundant.fasta-P2B10final.redundant.fasta-P2B11final.redundant.fasta-P2B12final.redundant.fasta-P2B1final.redundant.fasta-P2B2final.redundant.fasta-P2B3final.redundant.fasta-P2B4final.redundant.fasta-P2B5final.redundant.fasta-P2B6final.redundant.fasta-P2B7final.redundant.fasta-P2B8final.redundant.fasta-P2B9final.redundant.fasta-P2C10final.redundant.fasta-P2C11final.redundant.fasta-P2C12final.redundant.fasta-P2C1final.redundant.fasta-P2C2final.redundant.fasta-P2C3final.redundant.fasta-P2C4final.redundant.fasta-P2C5final.redundant.fasta-P2C6final.redundant.fasta-P2C7final.redundant.fasta-P2C8final.redundant.fasta-P2C9final.redundant.fasta-P2D10final.redundant.fasta-P2D11final.redundant.fasta-P2D12final.redundant.fasta-P2D1final.redundant.fasta-P2D2final.redundant.fasta-P2D3final.redundant.fasta-P2D4final.redundant.fasta-P2D5final.redundant.fasta-P2D6final.redundant.fasta-P2D7final.redundant.fasta-P2D8final.redundant.fasta-P2D9final.redundant.fasta-P2E10final.redundant.fasta-P2E11final.redundant.fasta-P2E12final.redundant.fasta-P2E1final.redundant.fasta-P2E2final.redundant.fasta-P2E3final.redundant.fasta-P2E4final.redundant.fasta-P2E5final.redundant.fasta-P2E6final.redundant.fasta-P2E7final.redundant.fasta-P2E8final.redundant.fasta-P2E9final.redundant.fasta-P2F10final.redundant.fasta-P2F11final.redundant.fasta-P2F12final.redundant.fasta-P2F1final.redundant.fasta-P2F2final.redundant.fasta-P2F3final.redundant.fasta-P2F4final.redundant.fasta-P2F5final.redundant.fasta-P2F6final.redundant.fasta-P2F7final.redundant.fasta-P2F8final.redundant.fasta-P2F9final.redundant.fasta-P2G1final.redundant.fasta-P2G2final.redundant.fasta-P2G3final.redundant.fasta-P2G4final.redundant.fasta, scale=totalgroup, label=0.03)
is not a valid group, and will be disregarded.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Cecum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Colon, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Duodenum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Duodenum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Ileum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Jejunum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Anaemia, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Cecum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Cecum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Cecum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Colon, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Colon, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Colon, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Duodenum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Duodenum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Faeces, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Ileum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Ileum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Ileum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Jejunum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Jejunum, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Control, group names must be unique. Please correct.
[ERROR]: Your design file contains more than 1 group named Jejunum, group names must be unique. Please correct.

any idea what is causing the error?

Thanks in advance

Solved! the problem was related to the tabular format in the design file. I had another query: in that same command, the option scale=totalgroup normalizes the relative abundance of each OTU in relation to the total number of sequences in each group?