Humann 3.9 conda install will not work. Please update your version of MetaPhlAn?

Microbial community profiling HUMAnN
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I installed humann3 according to instructions using conda. but there is an incompatability in the versions. Is there any way to actually get humann3 to run? If not can you please point me to instructions for installation / running that work. I used the ones here: " huttenhower.sph.harvard.edu/humann". then had to fix the ‘unknown command –bowtie2out’ , but I am now getting an error that the database versions do not match. I have not changed or specified anything.. I downloaded the databases and ran:

humann --input test.fastq --output humann-test/ --threads 8

which gave:

ERROR: The MetaPhlAn taxonomic profile provided was not generated with the expected database version. Please update your version of MetaPhlAn to at least v3.0.

ERROR: The MetaPhlAn taxonomic profile provided was not generated with the expected database version. Please update your version of MetaPhlAn to at least v3.0.

An example log is attached.

endia50.log.txt (4.3 KB)

Thanks for any help.

It is very frustrating not being able to run humann3 at all.

ERROR: The MetaPhlAn taxonomic profile provided was not generated with the expected database version. Please update your version of MetaPhlAn to at least v3.0
2

It looks like you’re running HUMAnN 3 with MetaPhlAn 4.2. We currently don’t have any version of HUMAnN compatible with MetaPhlAn 4.2 (but are working on this). I think for most people it makes sense to run HUMAnN 3 with MetaPhlAn 3, though later HUMAnN 3.x releases are compatible with specific MetaPhlAn 4 versions and marker databases. Please see the associated HUMAnN 3.x release notes for recommendations (they are posted here on the forum).

1 Like
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Hi, I don’t understand how exactly to fix it. I am using humann v3.9 and MetaPhlAn version 4.0.6 (1 Mar 2023). I have also installed metaphlan versiob vJun23 but looks like it is not being used and I keep getting this error: ERROR:

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.

How am I supposed to direct metaphlan to use vjun 23 database version?

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@franzosa ,

An update to my post.

I realized my MetaPhlAn 4.0.6 is actually older than vJun23 database support, and that is the real problem. So I did the following:

$ conda remove metaphlan

$ conda install metaphlan=4.1

$ conda install humann=3.9

Then, Reinstall the database

$ metaphlan --install --index mpa_vJun23_CHOCOPhlAnSGB_202307 --bowtie2db humann3_db/metaphlan_db_vJun23

I was able to run the metaphlan test using:

$ metaphlan --input_type fastq examples/demo.fastq.gz --bowtie2db humann3_db/metaphlan_db_vJun23 --index mpa_vJun23_CHOCOPhlAnSGB_202307 -o test.txt

where test.txt starts with #mpa_vJun23_CHOCOPhlAnSGB_202307 as expected

but still can’t run the humann demo test:

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”

which tells me:

CRITICAL ERROR: Can not call software version for metaphlan

Would you please help me understand what I am missing?

Thanks!

Faezeh

Installing Baqlava
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Hi Faezeh,

I struggled with the same issue over the past few days, and the solution that worked for me was to use MetaPhlAn version 4.1.1, not 4.1.2. If you simply specify 4.1, the installer currently pulls 4.1.2, which seems to cause the problem.

After downgrading to 4.1.1, everything worked again. (Using HUMAnN 3.9)

Since several things have recently changed regarding HUMAnN and MetaPhlAn version compatibility, this might be something worth checking for others who encounter the same issue. (@franzosa )

Hope this helps!
Lydia

1 Like
6

Thank you so much!

It eventually worked! Really appreciate your help!

Sincerely,

Faezeh

7

Thank you @LPrunus !

Question, do you know how to update the metaphlan database folder so we could skip providing its index and bowtie2db path? I need to know how to update it as I get metaphlan database error when running baqlava.

Appreciate!

Faezeh