Using v4.2.4 and the –long-reads option, which requires the .fna to remain in place after database install, in order to build a Minimap2 index.
Here is the tail of the output:
Wed Mar 11 16:28:24 2026: Decompressing metaphlan_long_read_db/mpa_vJan25_CHOCOPhlAnSGB_202503_SGB.fna.bz2 into metaphlan_long_read_db/mpa_vJan25_CHOCOPhlAnSGB_202503_SGB.fna
Wed Mar 11 16:41:10 2026: Decompressing metaphlan_long_read_db/mpa_vJan25_CHOCOPhlAnSGB_202503_VSG.fna.bz2 into metaphlan_long_read_db/mpa_vJan25_CHOCOPhlAnSGB_202503_VSG.fna
Wed Mar 11 16:41:45 2026: Joining FASTA databases
[WARNING] Failed to launch x86-64-v3 version, staying with default
[WARNING] Failed to launch x86-64-v3 version, staying with default
Wed Mar 11 16:42:40 2026: Removing uncompressed databases metaphlan_long_read_db/mpa_vJan25_CHOCOPhlAnSGB_202503_SGB.fna
Wed Mar 11 16:42:42 2026: Removing uncompressed databases metaphlan_long_read_db/mpa_vJan25_CHOCOPhlAnSGB_202503.fna
Wed Mar 11 16:42:44 2026: Download complete.
Wed Mar 11 16:43:38 2026: [Error] No Metaphlan database found at: metaphlan_long_read_db/mpa_vJan25_CHOCOPhlAnSGB_202503.fna to build the minimap index
Wed Mar 11 16:43:38 2026: Stop execution.
As you can see, MetaPhlAn first removes the uncompressed FNA file, and then a few lines later, complains that the .fna file does not exist.
Well sure it doesn’t, because you removed it 