I am facing the same problem too! Does anybody find a way to solve it? 
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Iâm using humann v3.6.1 and MetaPhlAn version 4.0.6 (1 Mar 2023), but face the same problem.
The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJan21 . Please update your version of MetaPhlAn to at least v3.0 or if you are using MetaPhlAn v4 please use the database vJan21.
Important! The MetaPhlAn 4 database has been substantially increased in comparison with the previous 3.1 version. Thus, for running MetaPhlAn 4, a minimum of 15GB or memory is needed.
ANSWER
If you have installed MetaPhlAn using Anaconda, it is advised to install the database in a folder outside the Conda environment. To do this, run
$ metaphlan --install --bowtie2db <database folder>
If you install the database in a different location, remember to run MetaPhlAn using --bowtie2db <database folder>!
By default, the latest MetaPhlAn database is downloaded and built. You can download a specific version with the --indexparameter
$ metaphlan --install --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db <database folder>
When --index is specified, MetaPhlAn skips the check for the latest database version and run the analysis using the database version provided by --index located in --bowtie2db.
This option is recommended when MetaPhlAn is run on HPC clusters or containerized
When --index is specified, MetaPhlAn skips the check for the latest database version and run the analysis using the database version provided by --index located in --bowtie2db.
This option is recommended when MetaPhlAn is run on HPC clusters or containerized
If you have issues in downloading the database, you can get it from:
Just download the .tar, .md5, and the mpa_latest files and place them in the metaphlan_databases folder.
Thank you @PabloGallardoM for your detailed post with the answer!
Hi @Katharina_Kujala, If you roll back your MetaPhlAn database to the vJan21 version it should resolve the error.
Thank you,
Lauren
@Katharina_Kujala Sorry I forgot to mention that upgrading to the latest HUMAnN version will provide a clearer error message.
Thank you,
Lauren
Thanks for the advice. But if I understood it right, I cannot actually use the newest MetaPhlAn DB if I want to run humann?
I actually found that when I just change the first line in the MetaPhlAn output to state an older database version, humann accepts it for some reason. So is there really any other problem with the MetaPhlAn output generated with the newest DB than the first line in the output file?
Thanks,
Katharina
@Katharina_Kujala Great questions! Yes, HUMAnN checks the version line in the MetaPhlAn file to make sure they are compatible. HUMAnN currently is only compatible with the MetaPhlAn vJan21 database and not yet the latest vOct22 database. There is a mapping file in HUMAnN with associations of SGBs to species that is specific to the MetaPhlAn vJan21 database which is why it checks the MetaPhlAn version. We are working on a new HUMAnN release which will be compatible with the latest MetaPhlAn database. We hope to have this ready soon and will post here when released.
Thanks!
Lauren
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Hello,
I tried as you said: Humann 3.6.1, Metaphlan 4.0.6 with database vJan21 But it still doesnât work.
Do I have to add the argument
âmetaphlan-options ââbowtie2db $PATHDBâ
Thanks for the help
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I think you would only need that option if you installed the database in a location other than the default. You would need the --index <version> option though to point to the vJan21 database.
Please post again if you continue to run into issues.
Thank you,
Lauren
Hello,
May I ask have you solved the problem? If so, could you share your solutions?
Thank you.
I ran the demo test successfully after installing the vJan21 database , with the parameters --metaphlan-options ââindex mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db $pathOfDownloadedvJan21databaseâ. I think then humann should be working normally.
Thanks for this answer and instructions. This should indeed be the way to do it, I would think.
Unfortunately, when running HUMAnN3.9 with MetaPhlAn 4.0.6 with and âindexingâ a previous version of the database (mpa_vJan21_CHOCOPhlAnSGB_202103), Iâm still getting the message:
The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJun23. Please update your version of MetaPhlAn to at least v3.0 or if you are using MetaPhlAn v4 please use the database vJun23.
This might be to do with HUMAnN version 3.9? Not sure, but Iâm not keen on this feature of HUMAnN/MetaPhlAn always trying to force users to use the latest database. I thought the --index should solved this issue, but for some reason itâs not working for me here (at least not with version 3.9).
We have an HPC (multiple users) and would indeed like to keep the database consistent and only update when we think the time is right.
The issue is that HUMAnN 3.X needs to use a compatibility file to understand the output of the latest MetaPhlAn 4.Y. We have tagged these compatibility files/modes to specific releases. Hence HUMAnN 3.9 will complain if youâre trying to feed it input from a MetaPhlAn 4.Y other than the one it was adapted for. If you maintain a fixed interoperable HUMAnN 3.X + MetaPhlAn 4.Y pair then you wonât have any issues, but if you upgrade one and not the other (or change the marker database) then HUMAnN will raise this warning.
As a side note, we are planning on adding a flag in a future release that will allow users to map against whatever database theyâd like without raising this warning (in a âproceed at your own riskâ sort of way).
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Thanks for the reply. Appreciate it.
So, if I understand you correctly, HUMAnN 3.9 (with MetaPhlAn 4) is now only compatible with MetaPhlAn database version from June 2023? And so, HUMAnN 3.9 is not backwards compatible with the previous versions of the MetaPhlAn database i.e. January 2021?