Qiime2 taking up so much disk space on host PC?


I’m running qiime2019.7 on a 64 bit Ubuntu machine, using VirtualBox6.0. My host laptop has 12gb RAM, of which I’ve allocated around 8gb to the virtual machine. It has 130GB storage space. I selected a dynamic disc storage for the virtual machine

Recently I noticed that the qiime2 core has suddenly become very big, (78GB) and has filled up almost all the disk space on the host, to the point where it can no longer boot or run properly. I deleted lots of files, including all the trash files and apps I don’t use, and then shrunk the machine to try and free up disk space. However after this, the qiime core had increased in size by 3gb. I’ve checked all my remaining files/folders and none of them seem particularly big. And I don’t have any snapshots

Does anyone have any idea why or what might be going on? And some possible solutions? How much space should Qiime2 typically take up on the host hard drive? This problem seems to have occured when I started to try and train my own feature classifiers, I have run denoising and diversity plugins without any problems so far.


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I suppose that your analysis was interrupted or failed once and because of it you have temporal leftovers on your storage, which should be deleted but remained due the interruptions (8 and even 12 Gb of RAM may be not enough for some tasks in Qiime, such as denoising or classifier training). The normal size on my machine for Qiime2 env is no more than 5 Gb. Please, check your storage for temporal files.
I don’t know, if it is a good advise, but I use BleachBit to clean my machine.


Hi @Bethanie,

Excuse me because I’m slightly less familiar with the virtual box, but I’ve had issues with my memory allocation on our cluster related to the /tmp/ folder. I do a hard clean of that

cd /tmp/
rm -r qiime*
rm -r q2*

And that tends to help some of my memory problems.