Metaphlan 4.2 currently won’t work with the long read option when downloading the database using metaphlan –install as this deletes the requires fasta file by default:
metaphlan --install --db_dir ~/dienerlab/refs/metaphlan
Tue Oct 28 13:00:44 2025: Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_latest
Tue Oct 28 13:00:44 2025: Downloading file of size: 0.0000 MB
Tue Oct 28 13:00:44 2025: MetaPhlAn database not present or partially present in /home/gpfs/o_diener/dienerlab/refs/metaphlan.
Downloading database
Please note due to the size this might take a few minutes.
Tue Oct 28 13:00:44 2025: Downloading and uncompressing bowtie2 indexes
Tue Oct 28 13:00:44 2025: Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vJan25_C
HOCOPhlAnSGB_202503_bt2.tar
Tue Oct 28 13:00:45 2025: Downloading file of size: 33433.5645 MB
Tue Oct 28 14:42:54 2025: Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vJan25_C
HOCOPhlAnSGB_202503_bt2.md5
Tue Oct 28 14:42:55 2025: Downloading file of size: 0.0001 MB
Tue Oct 28 14:42:55 2025: Checking md5 of /home/gpfs/o_diener/dienerlab/refs/metaphlan/mpa_vJan25_CHOCOPhlAnSGB_202503_bt2.md5
Tue Oct 28 14:42:55 2025: Checking md5 of /home/gpfs/o_diener/dienerlab/refs/metaphlan/mpa_vJan25_CHOCOPhlAnSGB_202503_bt2.tar
Tue Oct 28 14:56:10 2025: Downloading and uncompressing additional files
Tue Oct 28 14:56:10 2025: Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan25_CHOCOPhlAnSGB_202
503.tar
Tue Oct 28 14:56:10 2025: Downloading file of size: 4881.7773 MB
Tue Oct 28 15:01:40 2025: Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan25_CHOCOPhlAnSGB_202
503.md5
Tue Oct 28 15:01:40 2025: Downloading file of size: 0.0001 MB
Tue Oct 28 15:01:40 2025: Checking md5 of /home/gpfs/o_diener/dienerlab/refs/metaphlan/mpa_vJan25_CHOCOPhlAnSGB_202503.md5
Tue Oct 28 15:01:40 2025: Checking md5 of /home/gpfs/o_diener/dienerlab/refs/metaphlan/mpa_vJan25_CHOCOPhlAnSGB_202503.tar
Tue Oct 28 15:02:29 2025: Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan25_CHOCOPhlAnSGB_202
503.nwk
Tue Oct 28 15:02:29 2025: Downloading file of size: 2.0352 MB
Tue Oct 28 15:02:29 2025: Decompressing /home/gpfs/o_diener/dienerlab/refs/metaphlan/mpa_vJan25_CHOCOPhlAnSGB_202503_SGB.fna.bz
2 into /home/gpfs/o_diener/dienerlab/refs/metaphlan/mpa_vJan25_CHOCOPhlAnSGB_202503_SGB.fna
Tue Oct 28 15:11:17 2025: Decompressing /home/gpfs/o_diener/dienerlab/refs/metaphlan/mpa_vJan25_CHOCOPhlAnSGB_202503_VSG.fna.bz
2 into /home/gpfs/o_diener/dienerlab/refs/metaphlan/mpa_vJan25_CHOCOPhlAnSGB_202503_VSG.fna
Tue Oct 28 15:11:46 2025: Joining FASTA databases
Tue Oct 28 15:15:03 2025: Removing uncompressed databases /home/gpfs/o_diener/dienerlab/refs/metaphlan/mpa_vJan25_CHOCOPhlAnSGB
_202503_SGB.fna
Tue Oct 28 15:15:03 2025: Removing uncompressed databases /home/gpfs/o_diener/dienerlab/refs/metaphlan/mpa_vJan25_CHOCOPhlAnSGB
_202503.fna
Tue Oct 28 15:15:04 2025: Download complete.
Tue Oct 28 15:15:45 2025: The database is installed (mpa_vJan25_CHOCOPhlAnSGB_202503)
This will then result in a metaphlan error when running with the long reads option:
Tue Oct 28 15:31:20 2025: [Error] No Metaphlan database found at: /home/gpfs/o_diener/dienerlab/refs/metaphlan/mpa_vJan25_CHOCO
PhlAnSGB_202503.fna to build the minimap index
Tue Oct 28 15:31:20 2025: Stop execution.