Metaphlan ignores provided bowtie DB

Microbial community profiling MetaPhlAn
1

Describe the bug
MetaPhlAn totally ignores the installed Bowtie2 database and tries (and fails) to re-download one. This behavior has been duplicated (by me) using multiple databases, on both a cluster running Linux Alpine, and also with the official MetaPhlAn docker images.

To Reproduce

  1. Make a folder called my-awesome-data and in it, place corresponding R1 and R2 fastqz files, e.g., AP0F_ST2_S451_L004_R1_001.trimmed.fastq.gz and AP0F_ST2_S451_L004_R2_001.trimmed.fastq.gz.
  2. Install the docker image: docker pull biobakery/metaphlan
  3. Run the docker image with the provided files, like so (replacing /path/to/me with the result of pwd):
sudo docker run -it --rm \
     -v /path/to/me/my-awesome-data:/data \     
    biobakery/metaphlan metaphlan \
    /data/AP0F_ST2_MetaAir_S451_L004_R1_001.trimmed.fastq.gz, \ 
   /data/AP0F_ST2_MetaAir_S451_L004_R2_001.trimmed.fastq.gz \
     --input_type fastq \
     --bowtie2db /usr/local/lib/python3.6/dist-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103 \
    --bowtie2out /data/bowtie-output \
    --nproc 25 \
     -o /data/arbitrary-output.txt

And observe as it totally ignores the installed databases in /usr/local/lib/python3.6/dist-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103 and instead tries and fails to reinstall them:

Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_latest
Downloading file of size: 0.00 MB
0.01 MB 25600.00 %  31.36 MB/sec  0 min -0 sec         
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes

Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212.tar
Downloading file of size: 2884.91 MB
2884.91 MB 100.00 %   8.55 MB/sec  0 min -0 sec         
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212.md5
Downloading file of size: 0.00 MB
0.01 MB 11702.86 %  45.57 MB/sec  0 min -0 sec         

Decompressing /usr/local/lib/python3.6/dist-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103/mpa_vOct22_CHOCOPhlAnSGB_202212_VSG.fna.bz2 into /usr/local/lib/python3.6/dist-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103/mpa_vOct22_CHOCOPhlAnSGB_202212_VSG.fna


Decompressing /usr/local/lib/python3.6/dist-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103/mpa_vOct22_CHOCOPhlAnSGB_202212_SGB.fna.bz2 into /usr/local/lib/python3.6/dist-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103/mpa_vOct22_CHOCOPhlAnSGB_202212_SGB.fna


Joining FASTA databases

Building Bowtie2 indexes
Removing uncompressed databases

Download complete
No MetaPhlAn BowTie2 database found (--index option)!
Expecting location /usr/local/lib/python3.6/dist-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103/mpa_vOct22_CHOCOPhlAnSGB_202212

Screenshots
Not applicable.

Platform (please complete the following information):

  • Version is the latest image on Docker Hub. But I also replicated this behavior installing via conda and pip (I tried both!) on Alpine Linux. In the Docker image, I get:
(base) max@max-XPS-13-9310:~/projects/emily/get-phyloflash-to-work$ sudo docker run -it --rm biobakery/metaphlan metaphlan --version
MetaPhlAn version 4.0.2 (22 Sep 2022)
  • Download source is Docker Hub but also I tried both pip and conda.

Additional context
Happy to provide additional context if needed, but seeing as how the error can be directly reproduced using the publicly available Docker image, I think this should be sufficient.

I also reported this on Github Issues, but, it was auto-closed. When directed to post here I noticed you do not have any tag for bug reports. This should be rectified, IMHO. That being said, thank you for the help! We appreciate it.

2

You access the local directory /path/to/me/my-awesome-data as /data, so how about creating the database there?

metaphlan --install --bowtie2db /data/metaphlan_databases/vOct22
``

Once installed, you can use

sudo docker run -it --rm
-v /path/to/me/my-awesome-data:/data \
biobakery/metaphlan metaphlan
/data/AP0F_ST2_MetaAir_S451_L004_R1_001.trimmed.fastq.gz, \
/data/AP0F_ST2_MetaAir_S451_L004_R2_001.trimmed.fastq.gz
–input_type fastq
–bowtie2db /data/metaphlan_databases/vOct22
–bowtie2out /data/bowtie-output
–nproc 25
-o /data/arbitrary-output.txt


Without specifying the index, it installs the latest one, not vJan21.