# MetaPhlan 4 can not found BowTie2 database

**URL:** <https://forum.biobakery.org/t/metaphlan-4-can-not-found-bowtie2-database/4110>\
**Category:** MetaPhlAn\
**Created:** [September 23, 2022, 5:21pm UTC](https://forum.biobakery.org/t/metaphlan-4-can-not-found-bowtie2-database/4110 "2022-09-23T17:21:48Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![XiongGZ](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/xionggz/32/1672_2.png) [@XiongGZ](https://forum.biobakery.org/u/XiongGZ)\
**Post date:** [September 23, 2022, 5:21pm UTC](https://forum.biobakery.org/t/metaphlan-4-can-not-found-bowtie2-database/4110/1 "2022-09-23T17:21:48Z")

</div>

Version: 4.0.1

Command:

```auto
  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:

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

```

**Database check**  
Command:

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

```

Result:

```auto
The database is installed

```

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

---

<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [September 27, 2022, 7:33am UTC](https://forum.biobakery.org/t/metaphlan-4-can-not-found-bowtie2-database/4110/2 "2022-09-27T07:33:40Z")

</div>

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?

---

<div class="post-metadata">

**Author:** ![XiongGZ](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/xionggz/32/1672_2.png) [@XiongGZ](https://forum.biobakery.org/u/XiongGZ)\
**Post date:** [September 27, 2022, 7:55am UTC](https://forum.biobakery.org/t/metaphlan-4-can-not-found-bowtie2-database/4110/3 "2022-09-27T07:55:31Z")

</div>

Commands:

```auto
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](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/3/3f055a5dde7f239ddf3385db29dd028761894759.png)

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.)

---

<div class="post-metadata">

**Author:** ![Kborg000](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kborg000/32/3070_2.png) [@Kborg000](https://forum.biobakery.org/u/Kborg000)\
**Post date:** [January 22, 2025, 10:24pm UTC](https://forum.biobakery.org/t/metaphlan-4-can-not-found-bowtie2-database/4110/4 "2025-01-22T22:24:14Z")

</div>

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?