# Can I use the option --bowtie2out (for StrainPhlan!) along HUMANn?

**URL:** <https://forum.biobakery.org/t/can-i-use-the-option-bowtie2out-for-strainphlan-along-humann/8069>\
**Category:** HUMAnN\
**Created:** [May 16, 2025, 7:59pm UTC](https://forum.biobakery.org/t/can-i-use-the-option-bowtie2out-for-strainphlan-along-humann/8069 "2025-05-16T19:59:47Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![drelo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/drelo/32/566_2.png) [@drelo](https://forum.biobakery.org/u/drelo)\
**Post date:** [May 16, 2025, 7:59pm UTC](https://forum.biobakery.org/t/can-i-use-the-option-bowtie2out-for-strainphlan-along-humann/8069/1 "2025-05-16T19:59:47Z")

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Dear users,

I have HUMANn 3.8 installed and wanted to recover a taxonomic and functional profile with our samples. After I am looking at the StrainPhlan tutorial and I need to provide these options within metaphlan

```auto
metaphlan ${f} --input_type fastq -s sams/${bn}.sam.bz2 --bowtie2out bowtie2/${bn}.bowtie2.bz2 -o profiles/${bn}_profiled.tsv

```

I wonder if I can run HUMANn with these MetaPhlAn options so I can use StrainPhlan later on

`humann --input /run/media/andrespara/HUMANN/N06.fastq.gz --output ./OUT/N06 --threads 6 --metaphlan-options "--bowtie2db /home/andrespara/andres/nowmetaphlan -s ./SAMS/N06.sam.bz2 --bowtie2out ./BOWTIE2/N06.bowtie2.bz2" --memory-use minimum --nucleotide-database "/home/andrespara/andres/chocophlan"`

This worked partially since I got a **SAMS** folder an sam files but the **BOWTIE2** folder is empty. An additional question would be "Can I use the bowtie files within the humann\_temp folder to feed StrainPhlan?

Thanks

Best

Andrés

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<div class="post-metadata">

**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:** [May 16, 2025, 8:24pm UTC](https://forum.biobakery.org/t/can-i-use-the-option-bowtie2out-for-strainphlan-along-humann/8069/2 "2025-05-16T20:24:55Z")

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You can pass additional options to MetaPhlAn via HUMAnN using the `--metaphlan-options` flag. However, I find it’s often easier to just run MetaPhlAn outside of HUMAnN (using whatever parameters you’d like), and then pass the resulting taxonomic profile to HUMAnN via its `--taxonomic-profile` flag. It turns into a two-step process per sample, but it makes it a little easier to control each step.

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<div class="post-metadata">

**Author:** ![drelo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/drelo/32/566_2.png) [@drelo](https://forum.biobakery.org/u/drelo)\
**Post date:** [May 19, 2025, 8:35pm UTC](https://forum.biobakery.org/t/can-i-use-the-option-bowtie2out-for-strainphlan-along-humann/8069/3 "2025-05-19T20:35:39Z")

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Thanks for your help, I am now trying to run both HUMAn 4 and MetaPhlAn 4 I installed both software in the same environment and maybe that made it difficult to setup the databases (I got an error similar to [Humann database errors (a short novel) - #3 by RbccBstn](https://forum.biobakery.org/t/humann-database-errors-a-short-novel/7859/3)). I am currently re-downloading the metaphlan database to make it work but I wanted to thank you for this reply above.

Best

Andrès

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<div class="post-metadata">

**Author:** ![drelo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/drelo/32/566_2.png) [@drelo](https://forum.biobakery.org/u/drelo)\
**Post date:** [May 29, 2025, 8:24pm UTC](https://forum.biobakery.org/t/can-i-use-the-option-bowtie2out-for-strainphlan-along-humann/8069/4 "2025-05-29T20:24:40Z")

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Dear all,

I was trying to run the pipeline using first metaphlan and then humann 4 alpha.  
I installed diamond and also provided the route to the databases with `humann_config`

As per the documentation I tried the following:

**# 001**  
`metaphlan RAW/SRR14076335_1.fastq.gz --input_type fastq -s SAMS/SRR14076335.sam.bz2 --bowtie2out BOWTIE2/SRR14076335.bowtie2.bz2 -o BUGS/SRR14076335_profile.tsv --add_viruses --unclassified_estimation --index mpa_vOct22_CHOCOPhlAnSGB_202403 --bowtie2db ./CHOCO/mpa_vOct22_CHOCOPhlAnSGB_202403`  
**# 002**  
`bzip2 -d ./SAMS/SRR*`  
**# 003**  
`humann --input ./UNCOMPRESS/SRR14076335.sam --output ./FromSAMS/SRR14076335 --metaphlan-options "--bowtie2db ./CHOCO --index mpa_vOct22_CHOCOPhlAnSGB_202403" --nucleotide-database "./HUMANn/chocophlan" --threads 22`

I haven’t exhaustively searched older threads but is there anything wrong with the procedure above? Or is there an alternate way to pass the metaphlan output to humann?  
Thanks for the help,  
Best,

Andrés