Make.file error

Hello everyone,

I’m new to mothur, and trying to start analysing my data. I’'ve set the directory:

mothur > set.dir(input=/Users/User/Desktop/inputFiles)

Mothur’s directories:

and then tried to make.file:
mothur > make.file(inputdir=/Users/User/Desktop/inputFiles, type=fastq, prefix=stability)

But it gave me:
Setting input directory to: /Users/User/Desktop/inputFiles
FIND: Invalid switch
[ERROR]: /Users/User/Desktop/inputFiles\fileList.temp is blank. Please correct.
[WARNING]: Unable to find any fastq files in your directory.

I don´t know what happened. Can anyone help me? I have the fastq files in there.

Thanks a lot!


Hi Cat,

What’s the output when you do …

dir /Users/User/Desktop/inputFiles

Also, you shouldn’t need to do the set.dir command if you are going to provide the inputdir path to make.file.


Hi Pat

It happens this:

mothur > dir/Users/User/Desktop/inputFiles

[ERROR]: You are missing (
[ERROR]: Invalid.

What can I do?

Thanks a lot!


Sorry - can you run that command from outside of mothur in the command line? Also there’s a space between the “dir” and the first “/”


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