I'm using QIIME2 through Docker and ran into this problem. It happens that the feature-classifier is not working when using the provided SILVA database. However it works fine with Greengenes's. Any suggestions? The error is down below.. ##########################################################…

Hi @lumluk ! Thanks for posting, and thank you for posting the full error trace. This is a problem with your system, not with the classifier itself. The key line is at the very bottom: OSError: [Errno 28] No space left on device So you are running out of disc space! This makes sense — the SILVA da…

Hi @Nicholas_Bokulich , thank you for the reply. I relocate the tmp folder of the docker to my local machine, which have plenty of space, but it still not working. Now the error is gone, but it didn't produce any result (taxonomy) file either. Somehow the program terminated without having the savi…

Can you please re-run this variant of that command and provide any output? Thanks! docker run -t -i \ -v $(pwd):/data \ -v /Users/tmp:/tmp \ qiime2/core:2018.6 \ qiime feature-classifier classify-sklearn \ --i-classifier silva-132-99-515-806-nb-classifier.qza \ --i-reads rep-seqs.qz…

I've tried, no results either. However, I natively install qiime2 and the command works fine. Can it be docker's problem?

[image] lumluk: I’ve tried, no results either. Ah, bummer. [image] lumluk: Can it be docker’s problem? Either that, or it is related to something on your host system. If you can answer the questions I asked above, that would help steer us in the right direction: [image] thermokars…

I'm running docker on MacOS HighSierra

[image] lumluk: I’m running docker on MacOS HighSierra Ah ha! Okay, so let's circle back to your original problem: [image] lumluk: OSError: [Errno 28] No space left on device Setting a new tmp dir in your docker commands isn't going to fix that issue, and it might actually cause other…

Well, sounds like 208 GB still isn't enough, right? QIIME 2 isn't the only thing using this disk space (for example, in your screenshot it mentions that almost 70 GB are already in use from other docker containers and images).

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Silva-132-99-515-806-nb-classifier.qza OSError: [Errno 28] No space left on device

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