phylophlan.dmnd should be 178M, so I guess something went wrong with diamond during the database creation.
PhyloPhlAn automatically downloads the database file and the build the index at runtime. So, you can check that the in database folder you should have a folder named
phylophlan that contains:
phylophlan.faa (175M) and
phylophlan.faa.bz2 (65M). If this is the case, please remove the
phylophlan.dmnd and re-run PhyloPhlAn. If the above 2 files have different dimensions it might be that they were not properly downloaded, so you can remove the whole database folder
phylophlan and re-run PhyloPhlAn.
In re-runnning PhyloPhlAn please use the
--verbose param and store the output to a file, so that you should have any problem you can also provide the output file that can help understand what’s not working.