--mpa3 No MetaPhlAn BowTie2 database found

Microbial community profiling MetaPhlAn
1

When I use the --mpa3 option (to try to get viruses and eukaryotes), I get “No MetaPhlAn BowTie2 database found”. Do I have to use an actual metaphlan3 database? If so where is it available?

Thanks.

1 Like
2

I have tried downloading the older DB from Index of /biobakery4/metaphlan_databases

My command is:
metaphlan reads/123.fasta -o 123/ --input_type fasta --nproc 24 -t rel_ab_w_read_stats --tax_lev a --no_map --bt2_ps very-sensitive-local --min_alignment_len 50 --bowtie2db /g/data/nm31/db/metaphlan3/ -x mpa_vJan21_CHOCOPhlAnSGB_202103 --tmp_dir ./ --add_viruses --mpa3

No MetaPhlAn BowTie2 database found (–index option)!
Expecting location bowtie2db

My db folder contains:
mpa_vJan21_CHOCOPhlAnSGB_202103.1.bt2l
mpa_vJan21_CHOCOPhlAnSGB_202103.2.bt2l
mpa_vJan21_CHOCOPhlAnSGB_202103.3.bt2l
mpa_vJan21_CHOCOPhlAnSGB_202103.4.bt2l
mpa_vJan21_CHOCOPhlAnSGB_202103.md5
mpa_vJan21_CHOCOPhlAnSGB_202103.pkl
mpa_vJan21_CHOCOPhlAnSGB_202103.rev.1.bt2l
mpa_vJan21_CHOCOPhlAnSGB_202103.rev.2.bt2l
mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.fna
mpa_vJan21_CHOCOPhlAnSGB_202103_VINFO.csv
mpa_vJan21_CHOCOPhlAnSGB_202103_VSG.fna
mpa_vJan21_CHOCOPhlAnSGB_202103_marker_info.txt
mpa_vJan21_CHOCOPhlAnSGB_202103_species.txt

So, the issue is that without --mpa and with the new db (Oct22) metaphlan works, but I do not get any viruses or eukaryotes. With the older db (Jan21) and --mpa3 I get the error above.

Can you please clarify how we can use a metaphlan3 db to get eukaryotes and viruses?

Thanks,

Theo

3

By accident, I tried the following:

metaphlan reads/123.fasta -o 123/ --input_type fasta --nproc 24 -t rel_ab_w_read_stats --tax_lev a --no_map --bt2_ps very-sensitive-local --min_alignment_len 50 --bowtie2db /g/data/nm31/db/metaphlan3/mpa_vJan21_CHOCOPhlAnSGB_202103 -x mpa_vJan21_CHOCOPhlAnSGB_202103 --tmp_dir ./ --add_viruses --mpa3

metaphlan then downloaded the Jan21 db into a new folder /g/data/nm31/db/metaphlan3/mpa_vJan21_CHOCOPhlAnSGB_202103

Then gave an error again:

Download complete
No MetaPhlAn BowTie2 database found (–index option)!
Expecting location bowtie2db