Hi @Fabio_Marroni, thanks for the detailed report! I'm not sure what exactly is causing this issue with your temporary directory. Can you please provide the output from running these commands (with your qiime2-2017.12 environment activated):
echo $TMPDIR $TEMP $TMP
python -c 'import tempfile; print(tempfile.gettempdir())'
ls -la /projects/novabreed/share/marroni/tmp/
df -Th /projects/novabreed/share/marroni/tmp/
I suspect there may be an issue with permissions on your temporary directory, or the directory is running out of disk space when the qiime2 command is running and attempting to create temporary files. Thanks!