That's seems to be a little bit strange to me. Of course you can try with Docker and if it is works, then the problem not in space, but some kind of misterious compatibility issues.
Beside installing Docker, other options are:
- Use older version of Qiime2 (with older sklearn classifier)
- Try to install conda and Qiime2 into your working space instead of home directory.
- Add some Gb to your home quota.
If other mods have better ideas please add your suggestions 
