Metaphlan4 --mpa3 --add_viruses failed

Microbial community profiling MetaPhlAn
1

Hi all! I am trying to run MetaPhlan 4 by adding parameters: --add_viruses and --mpa3 to allow the profiling of viral organisms, and then it returns the error: No MetaPhlAn BowTie2 database found (–index option)! But if I remove these two parameters, it runs smoothly. Here I attach my command, the error, and the bowtie2 database I used.

  1. my commands:
metaphlan  $FQ_DIRECTORY/$SAMPLE.fastq.gz --nproc 16 --read_min_len 30 --input_type fastq --bowtie2out $SAMPLE.bowtie2.out -o $SAMPLE.metaphlan4.txt --bowtie2db /Databases/Metaphlan4 --mpa3 --add_viruses
  1. the error:
No MetaPhlAn BowTie2 database found (--index option)!
Expecting location bowtie2db
Exiting...
  1. Those files are within the Bowtie2 database.
mpa_latest                              
mpa_vJan21_CHOCOPhlAnSGB_202103.4.bt2l      mpa_vJan21_CHOCOPhlAnSGB_202103.rev.2.bt2l
mpa_vJan21_CHOCOPhlAnSGB_202103.1.bt2l  mpa_vJan21_CHOCOPhlAnSGB_202103.md5         mpa_vJan21_CHOCOPhlAnSGB_202103.tar
mpa_vJan21_CHOCOPhlAnSGB_202103.2.bt2l  mpa_vJan21_CHOCOPhlAnSGB_202103.pkl         mpa_vJan21_CHOCOPhlAnSGB_202103_VINFO.csv
mpa_vJan21_CHOCOPhlAnSGB_202103.3.bt2l  mpa_vJan21_CHOCOPhlAnSGB_202103.rev.1.bt2l  mpa_vJan21_CHOCOPhlAnSGB_202103_VSG.fna

Really appreciate your help and time! Thanks in advance!

2

Hi @Nirvana
Currently, the metaphlan4 vJan21 database do not profile viral species. For using the --add_viruses parameter (together with the --mpa3 parameter) you should use the metaphlan 3.0 (or 3.1) database available here: Index of /biobakery3/metaphlan_databases