Running Batch mode for 16s rRNA SOP

Hi, I know this question is similar to another old post but I am still struggling! (how to run batch mode?)

I am very new to mothur, and I’ve managed to follow the 16s rRNA SOP, then I noticed there is instructions for a batch mode which (I assume) would be able to complete all the operations from the SOP in one go.

How do you run this command? One comment says to run stability.batch before starting mothur, but what does this mean?
Please could someone explain how to run this to me like I am five, it would be a huge help!

Thank you so much!

Hi Maria,

Thanks for your question! From the command prompt - outside of mothur - you’ll run …

mothur.exe stability.batch


./mothur stability.batch

The first example is for windows and the second is for Mac or Linux. You’ll need to have both the mothur program, stability.batch, and everything needed to run the commands in stability.batch inside of your current working directory. In other words if you run dir (windows) or ls at the command prompt, you should see your files listed in the output.

Hope this helps!

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Hi Pat,

Thanks for the help, I’ve managed to run it from the windows command line and it seems to run pretty well!

I had a small issue with it trying to use the old trainset file from the SOP (9_0321012), whereas I has the newer version (18_062020), is there a way to alter the batch code to use the new file or should I just use the old version?

Thanks again!

Hi Maria,

That’s great! You can edit the batch file to use the new trainset file and re run to use it.


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