# mpa\_v30\_CHOCOPhlAn\_201901 missing (but mpa\_v31\_CHOCOPhlAn\_201901 present instead)

**URL:** <https://forum.biobakery.org/t/mpa-v30-chocophlan-201901-missing-but-mpa-v31-chocophlan-201901-present-instead/4808>\
**Category:** HUMAnN\
**Created:** [February 16, 2023, 5:57pm UTC](https://forum.biobakery.org/t/mpa-v30-chocophlan-201901-missing-but-mpa-v31-chocophlan-201901-present-instead/4808 "2023-02-16T17:57:33Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![rda](https://avatars.discourse-cdn.com/v4/letter/r/c2a13f/32.png) [@rda](https://forum.biobakery.org/u/rda)\
**Post date:** [February 16, 2023, 5:57pm UTC](https://forum.biobakery.org/t/mpa-v30-chocophlan-201901-missing-but-mpa-v31-chocophlan-201901-present-instead/4808/1 "2023-02-16T17:57:33Z")

</div>

```auto
$ metaphlan --version
MetaPhlAn version 3.0.7 (09 Dec 2020)
$ humann --version
humann v3.0.0.alpha.4
$ biobakery_workflows --version
biobakery_workflows v3.0.0-alpha.7

```

When attempting to run:

```auto
biobakery_workflows_databases --install wmgx

```

according to: [Installing the workflows with pip · biobakery/biobakery\_workflows Wiki · GitHub](https://github.com/biobakery/biobakery_workflows/wiki/Installing-the-workflows-with-pip)

I get:

```auto
Could not locate a Bowtie index corresponding to basename "/u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901"

```

looking in /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan\_databases/ I see the following:

```auto
$ ls /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.
mpa_v31_CHOCOPhlAn_201901.1.bt2 mpa_v31_CHOCOPhlAn_201901.3.bt2 mpa_v31_CHOCOPhlAn_201901.fna.bz2 mpa_v31_CHOCOPhlAn_201901.pkl mpa_v31_CHOCOPhlAn_201901.rev.2.bt2
mpa_v31_CHOCOPhlAn_201901.2.bt2 mpa_v31_CHOCOPhlAn_201901.4.bt2 mpa_v31_CHOCOPhlAn_201901.md5 mpa_v31_CHOCOPhlAn_201901.rev.1.bt2 mpa_v31_CHOCOPhlAn_201901.tar

```

indeed the step:

```auto
metaphlan --install --nproc 2

```

does not download the version 30 of the DB but only the 31 as you can see from:

```auto
$ metaphlan --install --nproc 2

Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_latest
Downloading file of size: 0.00 MB
0.01 MB 31507.69 % 55.54 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/biobakery3/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.tar
Downloading file of size: 407.85 MB
Building a SMALL index85 MB/sec 0 min 0 sec         
407.85 MB 100.00 % 2.85 MB/sec 0 min 0 sec         
Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.md5
Downloading file of size: 0.00 MB
0.01 MB 12800.00 % 186.18 MB/sec 0 min -0 sec         

Decompressing /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.fna.bz2 into /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.fna

Building Bowtie2 indexes
Removing uncompress database /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.fna

Download complete
The database is installed

```

Is it possible that the metaphian DB has been updated from version 30 to 31 and that biobakery needs to be updated? Or should I do a manual download from [Index of /biobakery3/metaphlan\_databases](http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/)?

Thanks,

RD

---

<div class="post-metadata">

**Author:** ![rda](https://avatars.discourse-cdn.com/v4/letter/r/c2a13f/32.png) [@rda](https://forum.biobakery.org/u/rda)\
**Post date:** [February 16, 2023, 8:23pm UTC](https://forum.biobakery.org/t/mpa-v30-chocophlan-201901-missing-but-mpa-v31-chocophlan-201901-present-instead/4808/2 "2023-02-16T20:23:36Z")

</div>

The issue is with `biobakery_workflows_databases.py` and `shotgun.py` that have the version of the metaphlan\_databases hardcoded, a solution would be to read the version from `/PATH/TO/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_latest`:

```auto
$ grep -R metaphlan /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/biobakery_workflows/* | grep 30
/u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/biobakery_workflows/biobakery_workflows_databases.py: strainphlan_db=os.path.join(os.path.dirname(metaphlan. __file__ ),"metaphlan_databases","mpa_v30_CHOCOPhlAn_201901")
/u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/biobakery_workflows/tasks/shotgun.py: strainphlan_pkl=os.path.join(os.path.dirname(metaphlan. __file__ ),"metaphlan_databases","mpa_v30_CHOCOPhlAn_201901.pkl")

```