Mothur SOP Crash to Desktop

Hello, I am new at using Mothur and I am working through the MiSeq SOP. I have gotten to the part where it asks the user to redo the OTU-Analysis on the ASV file that is created. I am trying to rune the rarefaction.single command on the ASV file. I have done this several times and each time I try to run the command, it will tell me that it is using 16 processors, stay like that for a minute and then it crashes to my desktop. I have been told by my PI that it sounds like I am running out of memory, which I have checked. According to my computer, I have 15.7 GB out of the total 16 GB available.

I am working with mothur v.1.48.0 and the command I am trying to use is as follows:
mothur> rarefaction.single(, calc=sobs, freq=100)

I would really appreciate some help with this. Thank you very much.

Hi there,

What type of computer do you have? What’s the total number of ASVs in your analysis? How many groups?

You might try running it with fewer processors and see what happens.


I have an HP Victus running Microsoft 11. I am running the ASVs from the MiSeq SOP, so I am led to believe that I have 2403 ASV’s. I am not sure about the number of groups, I am looking at my text file that it generated and I am going to estimate around 20-30.

I have run it on 8 processors instead of the 16 processors and it will still crash to the desktop. Should I go lower? 4 or 2 processors?

I was told there is a way to see what processors are being used when I run a command in Mothur and I have not been able to figure out how to see that. I am not sure if that can be found on an HP machine or not.

Unfortunately, my knowledge of windows is pretty limited. My understanding is that it caps the amount of ram available to each program. So although you may have 16GB of ram on your computer, mothur may only have access to 4GB of that ram. You’d likely have to look at the activity monitor tool to see what it’s using. For bigger datasets, I generally recommend that people use a linux computer to overcome these and other problems. Perhaps using the linux subsystem on your windows computer would get you further.


Great! I will give that a shot, thank you!

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