Hi Irene! Welcome to the QIIME2 forum and community. 
Sorry this took so long, my week has been a little crazy. 
Thank you so much for always providing such clear and detailed help requests! Posting on the forum is great because other users can get help. The formatting here is better, too!
After looking at the files that I have from you in my email, It looks like you are providing a taxonomy line like this 'OTU_207 k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae' in your extension tree taxonomy file which does not go down to genus and species. Normally, the taxonomy file would have g__unclassified;s__unclassified or g__unidentified;s__unidentified or something along those lines as placeholders so that a lot of the microbiome bioinformatics tools see things as consistent. This is a "standard", as you can imagine consistency is easier to work with in computer programming. You will need to repair your taxonomy file to have ';g__unclassified;s__unclassified' on all the lines just as placeholders. You can find concatenate functions in Excel to add this string to each line or do this in Python. I'm not sure your computational level, so if you cannot do this or find help in your lab, let me know.
Now, normally ghost-tree uses genera to make smaller groups of related fungi, but since you do not have genera (they're all unclassified), you will have to do a custom tree. I added this feature: Options for plugin inputs/arguments (ghost-tree progress) a while back but I have not tested it too much besides on smaller trees. You don't need to read the details, but you can see the cool images showing how the graft level option/flag creates trees at different taxonomic groupings. When you're in command line, type --help after your ghost-tree command, then you will see the option to graft at a higher level. So you will do --graft-level f in your case.
Luckily your tree will be fairly small, so make sure to open in a tree viewer and make sure the groups make sense to you after you create your custom tree. OTUs in the same family should be grouped together, of course!
. If they aren't let me know. I would also try to compare your diversity analysis results if you plan to do them to non-phylogenetic or taxonomic diversity analysis methods such as bray-curtis or binary-jaccard.
Let me know if you have any other questions, and feel free to email me any cool results. Would love to see them. 