# Installing Baqlava

**URL:** <https://forum.biobakery.org/t/installing-baqlava/8768>\
**Category:** BAQLaVa\
**Created:** [February 10, 2026, 8:19pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768 "2026-02-10T20:19:21Z")\
**Posts on this page:** 20\
**Page:** 1

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [February 10, 2026, 8:19pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/1 "2026-02-10T20:19:21Z")

</div>

Hi,

I have been trying to install baqlava. First I installed humann v4.0.0.alpha.1. However, I am unable to install anadama2 (as a pre-requiry) properly –\> doesn’t give any error but doesn’t show any output when hitting anadama2 –help. Do I need to install any specific version of anadama?

Thanks!

Faezeh

---

<div class="post-metadata">

**Author:** ![jjensen44](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jjensen44/32/3298_2.png) [@jjensen44](https://forum.biobakery.org/u/jjensen44)\
**Post date:** [February 11, 2026, 4:12pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/2 "2026-02-11T16:12:37Z")

</div>

Hi Faezeh! BAQLaVa is not yet compatible with HUMAnN 4, please install v3.9. It is in the works to get a 4.0 compatible version so we should have that soon but just not yet! Is your AnADAMA2\>=0.10.0?

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [February 11, 2026, 4:28pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/3 "2026-02-11T16:28:17Z")

</div>

Hi Jensen,

Thanks a lot for your prompt response! Yes, I tried different versions of AnADAMA2 and all were the same.

Regarding HUMAnN v3.9, would you please guide me with all the database that is compatible with it? I struggled a lot for that too and at the end found the solution in this topic:

> [@MetaPhlAn 4 + HUMAnN 4 compatibility](https://forum.biobakery.org/t/metaphlan-4-humann-4-compatibility/8523/7):
>
> Hello Biobakers, I am wondering if you have some updates on this? Many thanks!

---

<div class="post-metadata">

**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [February 11, 2026, 7:22pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/4 "2026-02-11T19:22:21Z")

</div>

Hi @Faeze_Darbaniyan ,

Thank you so much for reaching out to the bioBakery Lab. Re: For the `anadama2` issue, I do not think the command `anadama2 –-help` will show the installed version or `help` options.

Can you type the following commands to test if anadama2 is installed in your system?

> python  
> import anadama2  
> print(anadama2. **version** )

Regards,  
Sagun

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [February 12, 2026, 4:48pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/5 "2026-02-12T16:48:26Z")

</div>

> [@sagunmaharjann](#):
>
> python

Hi Sagun,

Thanks a lot for your prompt response!

When I try to install it using _$ conda install -c bioconda anadama2_ inside the environment that I have installed HUMAaN 4, everything looks like to be working: _# All requested packages already installed_.

However, when I try _$import anadama2_ I get _ModuleNotFoundError: No module named ‘leveldb’_

And for _print(anadama2. **version** )_ I get _NameError: name ‘anadama2’ is not defined_

Would you please guide me from scratch if I need to do it in a different conda environment. The question is which database is compatible with HUMAaN older versions if I have to use older HUMAaN version.

Thanks!

Faezeh

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [February 17, 2026, 5:29pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/6 "2026-02-17T17:29:02Z")

</div>

> [@Faeze\_Darbaniyan](#):
>
> conda install -c bioconda anadama2

Dear @sagunmaharjann ,

I just wanted to update that I could overcome the leveldb error by running:

$ conda install -c conda-forge python-leveldb

Then, installed anadama2 using:

$ conda install -c bioconda anadama2

Now, trying the command you suggested gives me:

$ python

Python 3.12.12 | packaged by conda-forge | (main, Oct 22 2025, 23:25:55) [GCC 14.3.0] on linux

Type “help”, “copyright”, “credits” or “license” for more information.

\>\>\> import anadama2

\>\>\> print(anadama2.version)

Traceback (most recent call last):

File “”, line 1, in

AttributeError: module ‘anadama2’ has no attribute ‘version’

Is there something I am missing?

Thanks a lot!

Faezeh

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [February 23, 2026, 10:48pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/7 "2026-02-23T22:48:31Z")

</div>

Hi @jjensen44 ,

I am still struggling with having this working. I have also tried installing humann 3.9 but faced difficulty with its compatibility with metaphlan… Went through all related topics in the forum but no success. I was wondering if I should expect any updates from you.

Thanks a lot!

Faezeh

---

<div class="post-metadata">

**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [February 24, 2026, 4:42pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/8 "2026-02-24T16:42:30Z")

</div>

Hi @Faeze_Darbaniyan ,

Apologies you are still running into the installing issues for baqlava and its dependencies (humann and metaphlan). I see that you are now using `humann v3.9` and `metaphlan v4.1` with `mpa_vJun23_CHOCOPhlAnSGB_202307` database [in this post](https://forum.biobakery.org/t/humann-3-9-conda-install-will-not-work-please-update-your-version-of-metaphlan/8484/4) which is the correct path forward for `baqlava` installation.

Since `metaphlan v4.1` demo is running as expected and `humann v3.9` demo is not, this error usually happens when HUMAnN can’t properly run `metaphlan --version`, often because of an environment mismatch or small formatting issues in the command.

Could you quickly run:

```auto
which humann
which metaphlan
metaphlan --version

```

and confirm they’re coming from the same `conda` environment? Also, please try retyping the HUMAnN command manually just to avoid any hidden special characters(`quotes`).

Let me know what you see and we’ll sort it out.

Regards,  
Sagun

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [February 25, 2026, 4:56pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/9 "2026-02-25T16:56:57Z")

</div>

Thank you so much @sagunmaharjann for your help!

Here is the output of what you asked for:

(humann3) [fdarbaniyan@ldragon3 ~]$ which humann

~/Rafael/install/ls/envs/humann3/bin/humann

(humann3) [fdarbaniyan@ldragon3 ~]$ which metaphlan

~/Rafael/install/ls/envs/humann3/bin/metaphlan

(humann3) [fdarbaniyan@ldragon3 ~]$ metaphlan --version

MetaPhlAn version 4.1.2 (16 Oct 2025)

No complete MetaPhlAn Bowtie2 database found

And I also retyped everything manually and still receive same error: CRITICAL ERROR: Can not call software version for metaphlan

Thanks!

Faezeh

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [February 27, 2026, 8:04pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/10 "2026-02-27T20:04:53Z")

</div>

Dear @sagunmaharjann ,

I also wanted to add that my metaphlan index is as follows:

```auto
total 23407904
-rw-rw-r-- 1 4389008193 Aug 3 2023 mpa_vJun23_CHOCOPhlAnSGB_202307.1.bt2l
-rw-rw-r-- 1 5634079508 Aug 3 2023 mpa_vJun23_CHOCOPhlAnSGB_202307.2.bt2l
-rw-rw-r-- 1 126529023 Aug 3 2023 mpa_vJun23_CHOCOPhlAnSGB_202307.3.bt2l
-rw-rw-r-- 1 2817039751 Aug 3 2023 mpa_vJun23_CHOCOPhlAnSGB_202307.4.bt2l
-rw-rw-r-- 1 98290559 Nov 27 2023 mpa_vJun23_CHOCOPhlAnSGB_202307.pkl
-rw-rw-r-- 1 4389008193 Aug 3 2023 mpa_vJun23_CHOCOPhlAnSGB_202307.rev.1.bt2l
-rw-rw-r-- 1 5634079508 Aug 3 2023 mpa_vJun23_CHOCOPhlAnSGB_202307.rev.2.bt2l
-rw-rw-r-- 1 44092 Nov 27 2023 mpa_vJun23_CHOCOPhlAnSGB_202307_VINFO.csv
-rwx------ 1 881484571 Feb 20 16:27 mpa_vJun23_CHOCOPhlAnSGB_202307_VSG.fna

```

Please let me know if I am missing anything.

Thanks!

Faezeh

---

<div class="post-metadata">

**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [February 27, 2026, 8:33pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/11 "2026-02-27T20:33:38Z")

</div>

Hello @Faeze_Darbaniyan ,

Thank you for trying the commands and follow up. Everything looks good with the software installation. Can you try with moving the metaphlan database to default path where metaphlan is expecting the databases please?

Example Demo command without having to pass bowtie2 index flag:

`$ metaphlan example.fastq --input_type fastq -o profiled_metagenome.txt`

Regards,  
Sagun

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [March 2, 2026, 7:27pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/12 "2026-03-02T19:27:29Z")

</div>

Thanks @sagunmaharjann for your reply!

I just moved the metaphlan database to the default path (substituted vJun23 with vJan25 version). Now I have the following as expected:

```auto
$ metaphlan --version
MetaPhlAn version 4.1.2 (16 Oct 2025)
Installed databases: mpa_vJun23_CHOCOPhlAnSGB_202307

```

Trying your command gives me the following error:

```auto
ERROR: Cannot find a local database. Please run MetaPhlAn using option "-x <database_name>".
            You can download the MetaPhlAn database from 
 http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases 

```

Checking it with database path I get:

```auto
$ metaphlan --input_type fastq examples/demo.fastq.gz --bowtie2db humann3_db/metaphlan_db_vJun23 --index mpa_vJun23_CHOCOPhlAnSGB_202307 -o profiled_metagenome.txt
[WARNING] Failed to launch x86-64-v3 version, staying with default
[WARNING] Failed to launch x86-64-v3 version, staying with default
[WARNING] Failed to launch x86-64-v3 version, staying with default
[WARNING] Failed to launch x86-64-v3 version, staying with default
WARNING: The metagenome profile contains clades that represent multiple species merged into a single representant.
An additional column listing the merged species is added to the MetaPhlAn output.

```

And checking the humann example, I have:

```auto
$ humann -i examples/demo.fastq.gz -o examples/SAMPLE2 --threads 16 --protein-database humann3_db/uniref --nucleotide-database humann3_db/chocophlan --metaphlan-options "–bowtie2db humann3_db/metaphlan_db_vJun23 -x mpa_vJun23_CHOCOPhlAnSGB_202307"
Output files will be written to: /rsrch6/home/hema_bio-Malignan/fdarbaniyan/Neeraj/HUMANN/examples/SAMPLE2
Decompressing gzipped file ...

CRITICAL ERROR: Can not call software version for metaphlan

```

Apparently, metaphlan and humann are still not connected.

Thanks!

Faezeh

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [March 9, 2026, 5:32pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/13 "2026-03-09T17:32:16Z")

</div>

Dear @sagunmaharjann ,

I realized that the issue comes from the version and I had to install metaphlan=4.1.1.

I also found the location where metaphlan database is installed and put vJun23 version there. But still when I try to run metaphlan without passing bowtie2 index flag as you proposed, I get:

```auto
ERROR: Cannot find a local database. Please run MetaPhlAn using option "-x <database_name>".

```

However, I can successfully run it when I provide biwtie2db and index.

The reason I need to overcome this is for baqlava. When I try it, I receive metaphlan database error which I don’t know how to overcome:

```auto
$ baqlava -i examples/demo.fq -o examples/output_demo --nucdb examples/BAQLaVa.V0.5.nucleotide/ --protdb examples/BAQLaVa.V0.5.protein/
Get error for metaphlan database

```

Thanks!

Faezeh

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [March 17, 2026, 6:13pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/14 "2026-03-17T18:13:38Z")

</div>

Hi @sagunmaharjann ,

I wonder if you got a chance to review this.

Thanks!

Faezeh

---

<div class="post-metadata">

**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [March 18, 2026, 3:58pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/15 "2026-03-18T15:58:18Z")

</div>

Hi @Faeze_Darbaniyan ,

The error suggests that `metaphlan` DB has still not been correctly installed in the machine locally. The correct metaphlan database install location would look like `<installed_location>/lib/python3.10/site-packages/metaphlan/metaphlan_databases/`. Can you confirm please if the databases are being installed in right location? This is critical for the next steps.

```auto
ERROR: Cannot find a local database. Please run MetaPhlAn using option "-x <database_name>".

```

Regards,  
Sagun

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [March 19, 2026, 5:25pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/16 "2026-03-19T17:25:37Z")

</div>

Hi @sagunmaharjann ,

Yes and here is the path I have for it:

```auto
$ ls My_installation_path/humann3/lib/python3.10/site-packages/metaphlan/metaphlan_databases
mpa_vJun23_CHOCOPhlAnSGB_202307.1.bt2l mpa_vJun23_CHOCOPhlAnSGB_202307.4.bt2l mpa_vJun23_CHOCOPhlAnSGB_202307.rev.2.bt2l
mpa_vJun23_CHOCOPhlAnSGB_202307.2.bt2l mpa_vJun23_CHOCOPhlAnSGB_202307.pkl mpa_vJun23_CHOCOPhlAnSGB_202307_VINFO.csv
mpa_vJun23_CHOCOPhlAnSGB_202307.3.bt2l mpa_vJun23_CHOCOPhlAnSGB_202307.rev.1.bt2l mpa_vJun23_CHOCOPhlAnSGB_202307_VSG.fna

```

I found this path by running `$ metaphlan --help` and coppied the databases there. Please let me know what I am missing.

Thanks!

Faezeh

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [March 25, 2026, 6:35pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/17 "2026-03-25T18:35:31Z")

</div>

Dear @sagunmaharjann ,

Any updates on this? May I ask the versions that are working for you?

Thanks!

---

<div class="post-metadata">

**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [March 27, 2026, 2:06pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/18 "2026-03-27T14:06:13Z")

</div>

Hi @Faeze_Darbaniyan ,

These are the current version that we are using/working on our side:

```auto
Loading module metaphlan4/4.1. (MetaPhlAn version 4.1.0 (23 Aug 2023))
Loading module humann3/3.9
Loading module anadama2/0.10.0
Loading module baqlava/0.5.0

```

```auto
#Metaphlan databases
total 52G

mpa_latest
mpa_previous
mpa_vJun23_CHOCOPhlAnSGB_202307.1.bt2l
mpa_vJun23_CHOCOPhlAnSGB_202307.2.bt2l
mpa_vJun23_CHOCOPhlAnSGB_202307.3.bt2l
mpa_vJun23_CHOCOPhlAnSGB_202307.4.bt2l
mpa_vJun23_CHOCOPhlAnSGB_202307_bt2.tar
mpa_vJun23_CHOCOPhlAnSGB_202307.pkl
mpa_vJun23_CHOCOPhlAnSGB_202307.rev.1.bt2l
mpa_vJun23_CHOCOPhlAnSGB_202307.rev.2.bt2l

pwd: /tools/metaphlan4/rocky8/v4.1/lib/python3.10/site-packages/metaphlan/metaphlan_databases/

```

Regards,  
Sagun

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [March 27, 2026, 5:16pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/19 "2026-03-27T17:16:42Z")

</div>

> [@sagunmaharjann](#):
>
> metaphlan example.fastq --input\_type fastq -o profiled\_metagenome.txt

Thanks @sagunmaharjann ,

I installed your version `(MetaPhlAn version 4.1.0 (23 Aug 2023))`

However, I am still unable to run metaphlan demo example without providing databases. Can you please create a new environment and try to re-install everything and see if it is reproducible? It is totally strange. Another issue regarding anadama2, here is what I get!

```auto
$ pip install anadama2
Requirement already satisfied: anadama2 in My_installation_path/humann3/lib/python3.10/site-packages (0.10.0)
Requirement already satisfied: networkx in My_installation_path/humann3/lib/python3.10/site-packages (from anadama2) (3.4.2)
Requirement already satisfied: leveldb in My_installation_path/humann3/lib/python3.10/site-packages (from anadama2) (0.201)
Requirement already satisfied: six in My_installation_path/humann3/lib/python3.10/site-packages (from anadama2) (1.17.0)
Requirement already satisfied: cloudpickle in My_installation_path/humann3/lib/python3.10/site-packages (from anadama2) (3.1.2)
Requirement already satisfied: pweave==0.25 in My_installation_path/humann3/lib/python3.10/site-packages (from anadama2) (0.25)
Requirement already satisfied: markdown in My_installation_path/humann3/lib/python3.10/site-packages (from anadama2) (3.10.2)
$ anadama2 --version
-bash: anadama2: command not found

```

---

<div class="post-metadata">

**Author:** ![Faeze\_Darbaniyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/faeze_darbaniyan/32/3546_2.png) [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\
**Post date:** [April 14, 2026, 3:10pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768/20 "2026-04-14T15:10:59Z")

</div>

Dear @sagunmaharjann ,

Any updates on this?

[Next page](https://forum.biobakery.org/t/installing-baqlava/8768.md?page=2)