MetaPhlan 4 can not found BowTie2 database

Microbial community profiling MetaPhlAn
1

Version: 4.0.1

Command:

  metaphlan $Data/00.Reads/soil/202009TB-N10_1.fastq.gz,$Data/00.Reads/soil/202009TB-N10_2.fastq.gz \
    --input_type fastq \
    --bowtie2out $Taxonomic_annotate/metaphlan/202009TB-N10.bowtie2.bz2 \
    --add_viruses --nproc 50 \
    -o $Taxonomic_annotate/metaphlan/202009TB-N10.txt

Error:

No MetaPhlAn BowTie2 database found (--index option)!
Expecting location bowtie2db
Exiting...

Database check
Command:

metaphlan --install --bowtie2db /opt/service/miniconda3/envs/vep_env/lib/python3.7/site-packages/metaphlan/metaphlan_databases

Result:

The database is installed

I have tried to add --index and/or --bowtie2db in the command, but returned the same error report.

2

Hi @XiongGZ
Could you show me the commands you use when adding the --index or the --bowtie2db ? can you also show me the content of the /opt/service/miniconda3/envs/vep_env/lib/python3.7/site-packages/metaphlan/metaphlan_databases folder?

3

Commands:

metaphlan --install --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db /opt/service/miniconda3/envs/vep_env/lib/python3.7/site-packages/metaphlan/metaphlan_databases

metaphlan --install --index mpa_vJan21_CHOCOPhlAnSGB_202103

metaphlan --install --bowtie2db /opt/service/miniconda3/envs/vep_env/lib/python3.7/site-packages/metaphlan/metaphlan_databases

Contents of the folder:

image
image1085×332 17.7 KB

Thanks for your help!
(I have solved this problem by using the custom database folder, and I found the default folder does not contain the *.bt2l files.)

4

Could either of you elaborate on the solution a bit?

I’m trying to setup biobakery_workflows and getting the same error. Is it expecting a bowtie2db subdirectory within the metaphlan_databases directory? Is it supposed to be separate but on the same level? If you made a custom directory, where would it go (same level?)? And what files exactly is it expecting to be in there?