# MetaPhlAn no relative abundance hnn4

**URL:** <https://forum.biobakery.org/t/metaphlan-no-relative-abundance-hnn4/7679>\
**Category:** HUMAnN\
**Created:** [December 19, 2024, 12:46pm UTC](https://forum.biobakery.org/t/metaphlan-no-relative-abundance-hnn4/7679 "2024-12-19T12:46:37Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Davide\_Bazzani](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/davide_bazzani/32/3113_2.png) [@Davide\_Bazzani](https://forum.biobakery.org/u/Davide_Bazzani)\
**Post date:** [December 19, 2024, 12:46pm UTC](https://forum.biobakery.org/t/metaphlan-no-relative-abundance-hnn4/7679/1 "2024-12-19T12:46:37Z")

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Hi,  
I was trying to run HUMAnN v4.0.0.alpha.1 installed following this guide ([HUMAnN 4.0.0.alpha.1 Release Notes - Google Docs](https://docs.google.com/document/d/1rCx5JkuO7wCKWrL8_-UJx_FkopJAfcDFtZktgPspak0/edit?tab=t.0#heading=h.i5hn0zprhwld)), but the software crashed after running MetaPhlAn prompting the folowing error:

> humann.search.prescreen - ERROR: The relative abundance and coverage were not found in the MetaPhlAn taxonomic profile. Please run MetaPhlAn with the option(s): --index mpa\_vOct22\_CHOCOPhlAnSGB\_202403 --bowtie2db /path/to/mpa/database.

I checked the taxonomic profile produced and it was fine.  
Here the first couples of lines of the profile:

> #SampleID Metaphlan\_Analysis  
> #clade\_name NCBI\_tax\_id relative\_abundance additional\_species  
> k\_\_Bacteria 2 100.0  
> k\_\_Bacteria|p\_\_Firmicutes 2|1239 84.08941  
> k\_\_Bacteria|p\_\_Bacteria\_unclassified 2| 12.284  
> k\_\_Bacteria|p\_\_Bacteroidetes 2|976 2.08048  
> k\_\_Bacteria|p\_\_Proteobacteria 2|1224 1.05261  
> k\_\_Bacteria|p\_\_Actinobacteria 2|201174 0.4935  
> k\_\_Bacteria|p\_\_Firmicutes|c\_\_Clostridia 2|1239|186801 83.5216  
> k\_\_Bacteria|p\_\_Bacteria\_unclassified|c\_\_Bacteria\_unclassified 2|| 12.284  
> k\_\_Bacteria|p\_\_Bacteroidetes|c\_\_Bacteroidia 2|976|200643 2.08048  
> k\_\_Bacteria|p\_\_Proteobacteria|c\_\_Betaproteobacteria 2|1224|28216 1.05261  
> k\_\_Bacteria|p\_\_Actinobacteria|c\_\_Coriobacteriia 2|201174|84998 0.4935  
> k\_\_Bacteria|p\_\_Firmicutes|c\_\_CFGB6645 2|1239| 0.32166  
> k\_\_Bacteria|p\_\_Firmicutes|c\_\_CFGB74538 2|1239| 0.18445  
> k\_\_Bacteria|p\_\_Firmicutes|c\_\_CFGB74524 2|1239| 0.0617

The databases I used were those suggested in the release note, in particular:

- mpa → mpa\_vOct22\_CHOCOPhlAnSGB\_202403

Here the code I used:

> humann --input /path/to/input/sample.fastq --output /path/to/output/ --nucleotide-database /path/to/nucleatide/database/chocophlan/ --protein-database /path/to/uniref/database/uniref --threads=16 --remove-temp-output --utility-database /path/to/utility/database/utility\_mapping --o-log /path/to/output/sample.log --metaphlan-options “–index mpa\_vOct22\_CHOCOPhlAnSGB\_202403 --bowtie2db /path/to/mpa/database”

In the pasted command lines, I masked my directories paths for data confidentiality, obviously when I ran the command I used the real paths.

Any idea why the software crashed?

I previously ran hnn3.9 on the same sample and it worked correctly.

Thanks

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**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [December 19, 2024, 4:09pm UTC](https://forum.biobakery.org/t/metaphlan-no-relative-abundance-hnn4/7679/2 "2024-12-19T16:09:26Z")

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I think the issue is because HUMAnN 4 now runs MetaPhlAn 4 using the `-t relab_with_read_stats` mode to get estimated SGB coverage. If you’re using the `--metaphlan-options` flag to specify arguments to the MetaPhlAn command, you would probably need to include the `-t` flag as well. Try that and let us know if it resolves the issue?

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**Author:** ![Davide\_Bazzani](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/davide_bazzani/32/3113_2.png) [@Davide\_Bazzani](https://forum.biobakery.org/u/Davide_Bazzani)\
**Post date:** [December 20, 2024, 10:43am UTC](https://forum.biobakery.org/t/metaphlan-no-relative-abundance-hnn4/7679/3 "2024-12-20T10:43:01Z")

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Hi,  
by adding the flag `-t relab_w_read_stats ` the software ran correctly!

Thanks

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**Author:** ![javadsadeghi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/javadsadeghi/32/2130_2.png) [@javadsadeghi](https://forum.biobakery.org/u/javadsadeghi)\
**Post date:** [April 4, 2025, 5:43pm UTC](https://forum.biobakery.org/t/metaphlan-no-relative-abundance-hnn4/7679/4 "2025-04-04T17:43:03Z")

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This also worked for me with the exception that now you should provide _ **-t rel\_ab\_w\_read\_stats** _