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!
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) 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
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!
We had some delay having the package available at conda but now the 4.0.0 should be already available: Metaphlan :: Anaconda.org
Hi @aitor.blancomiguez -
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
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.
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
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"
Dear Aitor,
Any update? can humann3 work with vOct22 now? Thanks.
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.
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