Make.file problem

Hi there,

I come here in search of your kindly help please.

I trying to analize some sequences, I saw the example called MiSeq_SOP and the first step in the analysis is to make a file of your sequences.

I am ashame because I can not start. I try the first step with the command make.file and the program responses:

“Ls” is not recognized as an internal or external command, program or executable batch file. Unable to find any fastq files in your directory.

Someone can help me please, what im doing bad?..

thank you very much in advance, best regards.


Here are the commands I used:

make.file(inputdir=MiSeq_SOP, type=fastq, prefix=stability)

Setting input directory to: MiSeq_SOP
“ls” no se reconoce como un comando interno o externo,
programa o archivo por lotes ejecutable.
[WARNING]: Unable to find any fastq files in your directory.

Output File Names:

Thank you all

You need to type


at the mothur prompt. Also, if you could post the English version of the error messages that would be helpful in the future.