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I start the Mothur Tutorial (https://www.mothur.org/wiki/MiSeq_SOP). But from the beginning, I got some error messages when I create " make.file "in mothur*(Error commands are shown below). I changed parameters but the result was negative. How can I solve this problem? 

****mothur > make.file(inputdir=MiSeq_SOP, type=fastq, prefix=stability)
Setting input directory to: MiSeq_SOP/
prefix is not a valid parameter.
The valid parameters are: type, seed, inputdir, and outputdir.
[ERROR]: did not complete make.file.****
Jay
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1 Answers1

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Actually, the prefix parameter is a valid parameter in mothur. Personally, I have never encountered a problem with using a prefix for the make.file command, but your command should be valid.

You could test if your inputdir is specified correctly (the mothur error and warning messages are not necessarily the most clear ones). If this works as well, I suggest that you well document this behaviour and send it to the mothur team (in my experience, they are quite responsive and ready to help).

bathyscapher
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