Hello
By referring to the metaphlan.py file, Metaphlan run requires two important database files: a .pkl file and a Bowtie2 index file.
I downloaded the file “mpa_vOct22_CHOCOPhlAnSGB_202403.tar”(http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202403.tar), and decompress, it includes a.pkl file, _SGB.fna.bz2, _VINFO.csv, and _VSG.fna.bz2.
The _SGB.fna.bz2 file contains 7,339,971 sequences.
But, in .pkl file, Its information is inconsistent with that of the previous _SGB.fna.bz2 file.
import pickle
import bz2
# open pkl file
db = pickle.load(bz2.open('mpa_vOct22_CHOCOPhlAnSGB_202403.pkl', 'r'))
db.keys()
#dict_keys(['taxonomy', 'markers', 'merged_taxon'])
#taxonomy
count_taxa = 0
for taxa in db['taxonomy']: count_taxa = count_taxa + 1
print(count_taxa) #30216 species
#markers
count_markers = 0
for marker in db['markers']: count_markers = count_markers + 1
print(count_markers) #5751328 marker gene
# in _SGB.fna.bz2 file contains 7,339,971 sequences.
So, please check this tar file.
