Problems with make.file during the try of MiSeq_SOP tutorial

Hi there.

I have just begun to try ‘MiSeq_SOP’ with the example data that can be downloaded from its webpage and I have encountered a problem (well, maybe not a problem, just a doubt) with the first command that appears in the SOP: make.file.

I have tried to generate my own ‘stability.files’, although there is one coming with the data. I run the mothur.exe from the same folder where the ‘MiSeq_SOP’ data folder is, not from another one copied ‘into’ that folder. So I type on the prompt

make.file(inputdir=MiSeq_SOP, type=fastq, prefix=stability2)

And as a result I get a file named ‘stability2.files’, as it was expected.

However, when I look it in deep I see that I have a file where all the rows in the first column are identical (“MiSeq”) and all the .fastq files (both the R1 and the R2) have a name begining with ‘MISEQ_SOP’.

Therefore, when trying to run the second command in the SOP, ‘make.contigs’, I get a result (‘Group count’) telling me that all the sequences belong to a unique sample, named ‘MISEQ’.

How can I do to make the command ‘make.file’ identifies the samples as different, I mean, match up the R1 and R2 from the same sample and then identify each sample in the inputdir as different?

Thanks a lot

I am having the same problem! I uploaded my own data after doing the tutorial and all my fastq files now have the directory name in front.

Glad I am not the only one with the issue!

I guess there should be a way to have the correct names in our data with this command.

However, if you do not have many samples, you can cahnge the names in a text editor before doing the


and it works.

Let’s wait for a better response, anyway :slight_smile:

There is a bug in make.file that will be corrected in the next release. The make.file command pairs the files properly, but the sample names are incorrect. As a workaround, you will have to manually change the sample names before running the make.contigs command.


Let’s wait then till the next release.

Thanks a lot