Installing Baqlava

Faeze_Darbaniyan · February 10, 2026, 8:19pm

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

jjensen44 · February 11, 2026, 4:12pm

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?

Faeze_Darbaniyan · February 11, 2026, 4:28pm

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:

sagunmaharjann · February 11, 2026, 7:22pm

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

Faeze_Darbaniyan · February 12, 2026, 4:48pm

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

Faeze_Darbaniyan · February 17, 2026, 5:29pm

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

Faeze_Darbaniyan · February 23, 2026, 10:48pm

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

sagunmaharjann · February 24, 2026, 4:42pm

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 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:

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

Faeze_Darbaniyan · February 25, 2026, 4:56pm

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

Faeze_Darbaniyan · February 27, 2026, 8:04pm

Dear @sagunmaharjann ,

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

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

sagunmaharjann · February 27, 2026, 8:33pm

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

Faeze_Darbaniyan · March 2, 2026, 7:27pm

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:

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

Trying your command gives me the following error:

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:

$ 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:

$ 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

Faeze_Darbaniyan · March 9, 2026, 5:32pm

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:

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:

$ 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

Faeze_Darbaniyan · March 17, 2026, 6:13pm

Hi @sagunmaharjann ,

I wonder if you got a chance to review this.

Thanks!

Faezeh

sagunmaharjann · March 18, 2026, 3:58pm

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.

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

Regards,
Sagun

Faeze_Darbaniyan · March 19, 2026, 5:25pm

Hi @sagunmaharjann ,

Yes and here is the path I have for it:

$ 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

Faeze_Darbaniyan · March 25, 2026, 6:35pm

Dear @sagunmaharjann ,

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

Thanks!

sagunmaharjann · March 27, 2026, 2:06pm

Hi @Faeze_Darbaniyan ,

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

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

#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

Faeze_Darbaniyan · March 27, 2026, 5:16pm

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!

$ 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

Faeze_Darbaniyan · April 14, 2026, 3:10pm

Dear @sagunmaharjann ,

Any updates on this?

Topic		Replies	Views
MinPath error with baqlava 0.5 metaphlan 3.1.0 and humann 3.9 BAQLaVa	2	62	December 4, 2025
Metaphlan database issue when running humann MetaPhlAn	2	226	May 16, 2024
How to install the latest metaphlan reference DB? MetaPhlAn	16	6230	March 23, 2023
Metaphlan V4.0.2 and Huma 3.6: MetaPhlAn taxonomic profile provided was not generated with the expected database HUMAnN	33	4973	April 29, 2024
No MetaPhlAn BowTie2 database found (--index option)! HUMAnN	22	8203	February 6, 2023

Installing Baqlava

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