# Cannot input custom taxonomic profile

**URL:** <https://forum.biobakery.org/t/cannot-input-custom-taxonomic-profile/3211>\
**Category:** MetaPhlAn\
**Created:** [February 23, 2022, 8:51pm UTC](https://forum.biobakery.org/t/cannot-input-custom-taxonomic-profile/3211 "2022-02-23T20:51:58Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![jorondo1](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jorondo1/32/1312_2.png) [@jorondo1](https://forum.biobakery.org/u/jorondo1)\
**Post date:** [February 23, 2022, 8:51pm UTC](https://forum.biobakery.org/t/cannot-input-custom-taxonomic-profile/3211/1 "2022-02-23T20:51:58Z")

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Hi,  
Trying to use --taxonomic-profile in Humann 3.0 yields this error :  
ERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the expected database version. Please update your version of MetaPhlAn2 to v3.0.

Is there a way to convert metaphlan2 reports to metaphlan3 ? my MPA file was generated via KrakenTools from a kraken report. From what I have read in [HUMAnN v3 joint taxonomic profile](https://forum.biobakery.org/t/humann-v3-joint-taxonomic-profile/480) they are not exactly the same…

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**Author:** ![thad](https://avatars.discourse-cdn.com/v4/letter/t/48db29/32.png) [@thad](https://forum.biobakery.org/u/thad)\
**Post date:** [February 23, 2022, 9:26pm UTC](https://forum.biobakery.org/t/cannot-input-custom-taxonomic-profile/3211/2 "2022-02-23T21:26:09Z")

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The first line of a MetaPhlAn3 output file,

#mpa\_v30\_CHOCOPhlAn\_201901

specifies the software version and ChocoPhlAn database version. You could try adding this line to your file. HUMANn3 will likely complain if it comes across a clade\_name that is not in the database.

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<div class="post-metadata">

**Author:** ![jorondo1](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jorondo1/32/1312_2.png) [@jorondo1](https://forum.biobakery.org/u/jorondo1)\
**Post date:** [February 23, 2022, 10:23pm UTC](https://forum.biobakery.org/t/cannot-input-custom-taxonomic-profile/3211/3 "2022-02-23T22:23:33Z")

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Hi, thanks a lot for your input. I have managed to figure that out and sharpen my (very basic) bash skills to convert the report this way :

awk ‘{printf("%s\t\n", $0)}’ temp.MPA.TXT | awk ‘BEGIN{printf("#mpa\_v30\_CHOCOPhlAn\_201901\n")}1’ - \> bugs\_list.MPA.TXT; rm temp.MPA.TXT

HUMANN accepts that input. The prescreen is however somewhat crazy, saying :  
Found g\_\_Burkholderia.s\_\_Burkholderia\_sp.\_PAMC\_28687 : 303.00% of mapped reads  
Found g\_\_Burkholderia.s\_\_Burkholderia\_sp.\_PAMC\_26561 : 204.00% of mapped reads  
Found g\_\_Bradyrhizobium.s\_\_Bradyrhizobium\_erythrophlei : 202.00% of mapped reads  
Found g\_\_Lichenicola.s\_\_Lichenicola\_cladoniae : 144.00% of mapped reads  
Found g\_\_Granulicella.s\_\_Granulicella\_sp.\_WH15 : 35.00% of mapped reads  
Found g\_\_Granulicella.s\_\_Granulicella\_sp.\_5B5 : 32.00% of mapped reads  
Found g\_\_Granulicella.s\_\_Granulicella\_tundricola : 33.00% of mapped reads  
Found g\_\_Granulicella.s\_\_Granulicella\_mallensis : 30.00% of mapped reads  
Found g\_\_Terriglobus.s\_\_Terriglobus\_roseus : 28.00% of mapped reads  
Found g\_\_Acidisarcina.s\_\_Acidisarcina\_polymorpha : 19.00% of mapped reads  
Found g\_\_Paenibacillus.s\_\_Paenibacillus\_sp.\_E222 : 159.00% of mapped reads  
Found g\_\_Physcomitrium.s\_\_Physcomitrium\_patens : 1032.00% of mapped reads  
Found g\_\_Homo.s\_\_Homo\_sapiens : 155.00% of mapped reads  
Total species selected from prescreen: 13  
**Selected species explain 2376.00% of predicted community composition**

I imagine this is caused by Krake, whose profile includes reads spanning more than just the marker genes. I’m trying to figure out if that could affect the humann pipeline downstream.