# StrainPhlan clade "s\_\_Akkermansia\_muciniphila" not accepted and should provide in SGB format **URL:** \ **Category:** StrainPhlAn\ **Created:** [January 28, 2023, 1:27am UTC](https://forum.biobakery.org/t/strainphlan-clade-s-akkermansia-muciniphila-not-accepted-and-should-provide-in-sgb-format/4722 "2023-01-28T01:27:03Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![raminka](https://avatars.discourse-cdn.com/v4/letter/r/46a35a/32.png) [@raminka](https://forum.biobakery.org/u/raminka)\ **Post date:** [January 28, 2023, 1:27am UTC](https://forum.biobakery.org/t/strainphlan-clade-s-akkermansia-muciniphila-not-accepted-and-should-provide-in-sgb-format/4722/1 "2023-01-28T01:27:03Z")
I want to run strainphlan4 on my metagenomics data to get the strains of the “s\_\_Akkermansia\_muciniphila”. However, following the tutorial for strainohlan4 pipeline, the clades are specified in SGB format. So I cannot pass “s\_\_Akkermansia\_muciniphila” as the option of the extract\_marker step: extract\_markers.py -c s\_\_Akkermansia\_muciniphila or at the strainphlan step: strainphlan.py -c s\_\_Akkermansia\_muciniphila Instead of the “s\_\_Akkermansia\_muciniphila”, I have to pass “SGB9228” or “SGB9228” which I found in the " [mpa\_vJan21\_CHOCOPhlAnSGB\_202103\_species.txt.bz2](http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_species.txt.bz2) file corresponding to the “s\_\_Akkermansia\_muciniphila” species. I am wondering how am I supposed to use both of them in my strainphlan and excract\_marker run to get all the strains of the “s\_\_Akkermansia\_muciniphila”. ---
**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:** [January 31, 2023, 8:58am UTC](https://forum.biobakery.org/t/strainphlan-clade-s-akkermansia-muciniphila-not-accepted-and-should-provide-in-sgb-format/4722/2 "2023-01-31T08:58:46Z")
Hi @raminka As you can see in the strainphlan tutorial ([StrainPhlAn 4 · biobakery/MetaPhlAn Wiki · GitHub](https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-4)) in version 4, the clades (`-c`) should be specified at the SGB level (as some species might span multiple SGBs). in your case, you should pass `-c t__SGB9228` in both extract\_markers and strainphlan scripts ---
**Author:** ![imontero](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/imontero/32/3411_2.png) [@imontero](https://forum.biobakery.org/u/imontero)\ **Post date:** [September 4, 2024, 2:50pm UTC](https://forum.biobakery.org/t/strainphlan-clade-s-akkermansia-muciniphila-not-accepted-and-should-provide-in-sgb-format/4722/3 "2024-09-04T14:50:14Z")
and how it should be done to know which SGB corresponds to each clade? ---
**Author:** ![vitorheidrich](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/vitorheidrich/32/1891_2.png) [@vitorheidrich](https://forum.biobakery.org/u/vitorheidrich)\ **Post date:** [September 5, 2024, 10:21am UTC](https://forum.biobakery.org/t/strainphlan-clade-s-akkermansia-muciniphila-not-accepted-and-should-provide-in-sgb-format/4722/4 "2024-09-05T10:21:32Z")
Hi @imontero You can get them from the MetaPhlAn profile. You will have this file because you have to run MetaPhlAn in order to have the SAM files used as input for sample2markers in StrainPhlAn. ---
**Author:** ![imontero](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/imontero/32/3411_2.png) [@imontero](https://forum.biobakery.org/u/imontero)\ **Post date:** [September 5, 2024, 11:22am UTC](https://forum.biobakery.org/t/strainphlan-clade-s-akkermansia-muciniphila-not-accepted-and-should-provide-in-sgb-format/4722/5 "2024-09-05T11:22:53Z")
Metaphlan profile file gives Kingdom, Phylum,…Family… Species, but does not give SGB code to, for example s\_\_Bifidobacterium\_longum. I could find it downloading a fileform database that lists all taxa and all SGB code, but no one of the output files from mMtaphlan helped. ---
**Author:** ![Michal\_Puncochar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/michal_puncochar/32/2321_2.png) [@Michal\_Puncochar](https://forum.biobakery.org/u/Michal_Puncochar)\ **Post date:** [September 23, 2024, 1:31pm UTC](https://forum.biobakery.org/t/strainphlan-clade-s-akkermansia-muciniphila-not-accepted-and-should-provide-in-sgb-format/4722/6 "2024-09-23T13:31:13Z")
Maybe you’re running Metaphlan 3? Make sure you use Metaphlan 4 with Strainphlan 4.