# Input Specification if Pre-Existing MetaPhlAn Files

**URL:** <https://forum.biobakery.org/t/input-specification-if-pre-existing-metaphlan-files/2096>\
**Category:** HUMAnN\
**Created:** [May 18, 2021, 9:00am UTC](https://forum.biobakery.org/t/input-specification-if-pre-existing-metaphlan-files/2096 "2021-05-18T09:00:13Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Dario](https://avatars.discourse-cdn.com/v4/letter/d/bc79bd/32.png) [@Dario](https://forum.biobakery.org/u/Dario)\
**Post date:** [May 18, 2021, 9:00am UTC](https://forum.biobakery.org/t/input-specification-if-pre-existing-metaphlan-files/2096/1 "2021-05-18T09:00:13Z")

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> FAQs  
> 6. I already have MetaPhlAn output. Can I start HUMAnN 3.0 with the MetaPhlAn output?  
> Yes, use the --taxonomic-profile bugs\_list.tsv option

But, what should the user specify for `--input` which is mandatory? bowtie2out isn’t a valid option unlike it is for MetaPhlAn 3.

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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:** [May 18, 2021, 12:29pm UTC](https://forum.biobakery.org/t/input-specification-if-pre-existing-metaphlan-files/2096/2 "2021-05-18T12:29:06Z")

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`--input` would still be your FASTQ file (reads) in this case: providing MetaPhlAn output to HUMAnN just allows you to skip the first step in which HUMAnN would otherwise run MetaPhlAn _for you_.

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**Author:** ![Dario](https://avatars.discourse-cdn.com/v4/letter/d/bc79bd/32.png) [@Dario](https://forum.biobakery.org/u/Dario)\
**Post date:** [May 18, 2021, 11:00pm UTC](https://forum.biobakery.org/t/input-specification-if-pre-existing-metaphlan-files/2096/3 "2021-05-18T23:00:17Z")

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Ah, I see. Do you plan to include some short vignettes in future that demonstrate steps end-to-end?

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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:** [May 19, 2021, 4:13pm UTC](https://forum.biobakery.org/t/input-specification-if-pre-existing-metaphlan-files/2096/4 "2021-05-19T16:13:58Z")

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We have a HUMAnN tutorial here?

> **[biobakery/biobakery](https://github.com/biobakery/biobakery/wiki/humann)**
>
> humann

This covers the default workflow and a few common follow-up steps. Special options (like bypassing MetaPhlAn) are described in the manual but omitted from the Tutorial in the interest of brevity.

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**Author:** ![Dario](https://avatars.discourse-cdn.com/v4/letter/d/bc79bd/32.png) [@Dario](https://forum.biobakery.org/u/Dario)\
**Post date:** [May 20, 2021, 12:00am UTC](https://forum.biobakery.org/t/input-specification-if-pre-existing-metaphlan-files/2096/5 "2021-05-20T00:00:04Z")

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Ah, thanks for the link. I was only reading the HUMAnN repository but it is in biobakery.