# Metaphlan4 and the new version humann **URL:** \ **Category:** MetaPhlAn\ **Created:** [August 23, 2022, 5:57am UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985 "2022-08-23T05:57:43Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![wusan1234](https://avatars.discourse-cdn.com/v4/letter/w/85e7bf/32.png) [@wusan1234](https://forum.biobakery.org/u/wusan1234)\ **Post date:** [August 23, 2022, 5:57am UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/1 "2022-08-23T05:57:43Z")
I am greatful for noticing the metaphlan4 was updated! So can metaphlan4 can accept the results from metaphlan3? And when the new HUMAnN version will update, If I run some samples by Metaphlan4, the downstream analysis can analysis by Humann3 or waitting for the new version HumanN4 or etc. Thx! ---
**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:** [August 23, 2022, 12:34pm UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/2 "2022-08-23T12:34:32Z")
Hi @wusan1234 While MetaPhlAn 4 is still compatible with version 3 using the --mpa3 parameter together with the specification of the mpa3 DB with the --index parameter, by default it includes a new database spanning 26,970 species-level genome bins (SGBs, [Segata Lab - Computational Metagenomics](http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html)) with 4,992 of them taxonomically unidentified at the species level (uSGBs). The results of the new metaphlan 4 database are not compatible with humann3, but we are expecting to release pretty soon the new humann3.5 version that includes compatibility with the new database ---
**Author:** ![wusan1234](https://avatars.discourse-cdn.com/v4/letter/w/85e7bf/32.png) [@wusan1234](https://forum.biobakery.org/u/wusan1234)\ **Post date:** [August 23, 2022, 12:54pm UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/3 "2022-08-23T12:54:05Z")
thx for ur answer! hmmm, I noticed the tutorial about metaphlan4 showed we can install it via conda. I tried but only 3.1.0 was the newest version and the marker ref were v31\_2019, not vJan\_202103, so how can i install the new version, only by clone from github? thx! ---
**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:** [August 23, 2022, 1:07pm UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/4 "2022-08-23T13:07:39Z")
We had some delay having the package available at conda but now the 4.0.0 should be already available: [Metaphlan :: Anaconda.org](https://anaconda.org/bioconda/metaphlan) ---
**Author:** ![DEEPCHANDA7](https://avatars.discourse-cdn.com/v4/letter/d/eb9ed0/32.png) [@DEEPCHANDA7](https://forum.biobakery.org/u/DEEPCHANDA7)\ **Post date:** [August 23, 2022, 2:02pm UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/5 "2022-08-23T14:02:22Z")
Hi @aitor.blancomiguez - 1. I am not sure about what do you mean by “–index” parameter. Can you please explain what this parameter denotes? 2.Can we use database `mpa_v30_CHOCOPhlAn_201901` with MetaPhlAn 4 using `--mpa3` flag? If yes, how the command should look like in that case? Many thanks ---
**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:** [August 23, 2022, 3:34pm UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/6 "2022-08-23T15:34:28Z")
Hi @DEEPCHANDA7 The --index parameter is used in metaphlan to specify a specific version of the database you want to run. If not specified, MetaPhlAn will look for the latest version available. So, for running MetaPhlAn 4 with the v30 database, you will have to use the following additional parameters: `--mpa3 --index mpa_v30_CHOCOPhlAn_201901 --bowtie2db v30_db_dir` Being `v30_db_dir` the directory containing the v30 database. ---
**Author:** ![xiaorongsmile](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/xiaorongsmile/32/2080_2.png) [@xiaorongsmile](https://forum.biobakery.org/u/xiaorongsmile)\ **Post date:** [April 2, 2023, 6:32am UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/7 "2023-04-02T06:32:18Z")
Hi, how to specify a metaphlan4 database when run humann3? cause the latest version (vOct22) of metaphlan database not compatible with humann3. The problem is that even though i download the vJan21 database in the metaphlan4 install dir( in my cluster it’s /anaconda3/envs/bioinfo/lib/python3.9/site-packages/metaphlan/metaphlan\_databases) , when i run human3, Metaphlan automatically downloaded the latest version （vOct22） of the database again in the same directory, then i got the error: > `ERROR: 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` so how to fix this, thank you very much ---
**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:** [April 5, 2023, 2:19pm UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/8 "2023-04-05T14:19:31Z")
We are currently working in making humann3 compatible with version vOct22. In the meanwhile you can try to run humann with the option: `--metaphlan-options "-t -index mpa_vJan21_CHOCOPhlAnSGB_202103"` ---
**Author:** ![fanhuan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fanhuan/32/451_2.png) [@fanhuan](https://forum.biobakery.org/u/fanhuan)\ **Post date:** [August 17, 2023, 2:21am UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/9 "2023-08-17T02:21:54Z")
> [@xiaorongsmile](#): > > vOct22 Dear Aitor, Any update? can humann3 work with vOct22 now? Thanks. ---
**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 1, 2023, 12:07pm UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/10 "2023-09-01T12:07:15Z")
Hi @fanhuan , yes! the latest version of humann is compatible with oct22 ---
**Author:** ![arit\_mhp](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/arit_mhp/32/2389_2.png) [@arit\_mhp](https://forum.biobakery.org/u/arit_mhp)\ **Post date:** [September 1, 2023, 9:23pm UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/11 "2023-09-01T21:23:45Z")
Hi @aitor.blancomiguez , I found the latest version 3.8 in pip. Is it compatible with oct22 db? If not how can get the latest version of humann which is compatible with oct22? Thanks. ---
**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 22, 2023, 2:32pm UTC](https://forum.biobakery.org/t/metaphlan4-and-the-new-version-humann/3985/12 "2023-09-22T14:32:44Z")
Hi @arit_mhp the latest version of humann should already download automatically the database compatible with oct22. If it does not, please open a thread in the humann subforum