# Humann 3.0 and bowtie metaphlan output **URL:** \ **Category:** HUMAnN\ **Created:** [September 22, 2020, 12:00pm UTC](https://forum.biobakery.org/t/humann-3-0-and-bowtie-metaphlan-output/1049 "2020-09-22T12:00:44Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![nousiaso](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nousiaso/32/411_2.png) [@nousiaso](https://forum.biobakery.org/u/nousiaso)\ **Post date:** [September 22, 2020, 12:00pm UTC](https://forum.biobakery.org/t/humann-3-0-and-bowtie-metaphlan-output/1049/1 "2020-09-22T12:00:44Z")
Greetings i would like to ask, is it possible, from a separate run of metaphlan 3.0 to take the bowtie output and give it to humann 3.0 as an input file? Thank you in advance for your reply! ---
**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:** [September 22, 2020, 2:15pm UTC](https://forum.biobakery.org/t/humann-3-0-and-bowtie-metaphlan-output/1049/2 "2020-09-22T14:15:36Z")
If you give HUMAnN bowtie (SAM) output it will treat it as mappings of reads against pangenomes, whereas the MetaPhlAn bowtie output is a mapping to marker genes only. You can provide MetaPhlAn bowtie output to _MetaPhlAn_ to regenerate a species profile and then provide _that_ to HUMAnN via the `--taxonomic-profile` flag. This will avoid needed to restart a MetaPhlAn run from scratch inside or outside of HUMAnN. ---
**Author:** ![nousiaso](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nousiaso/32/411_2.png) [@nousiaso](https://forum.biobakery.org/u/nousiaso)\ **Post date:** [September 22, 2020, 8:36pm UTC](https://forum.biobakery.org/t/humann-3-0-and-bowtie-metaphlan-output/1049/3 "2020-09-22T20:36:55Z")
thank you appreciate it! ---
**Author:** ![Marc\_Hoeppner](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/marc_hoeppner/32/525_2.png) [@Marc\_Hoeppner](https://forum.biobakery.org/u/Marc_Hoeppner)\ **Post date:** [March 1, 2021, 2:29pm UTC](https://forum.biobakery.org/t/humann-3-0-and-bowtie-metaphlan-output/1049/4 "2021-03-01T14:29:32Z")
Hi, as a novice user, I didn’t quite follow that explanation. For a colleague, I am trying to add a Humann3 analysis as an optional step after Metaphlan3 profiling. The Metaphlan stage produces both a sam.bz2 file and a taxonomic profile (and Graphlan etc all work fine at the moment). When I pass both to Humann, I get: # Pathway J07447-L1\_S37\_L001\_Abundance UNMAPPED 0.0000000000 UNINTEGRATED 0.0000000000 So something is not working. If I only try to pass a taxonomic profile, Humann3 complains that it also needs “-i”. Metaphlan 3 is the latest version, installed in a Docker Container using the latest Chocophlan database from a local directory. Humann3 is currently installed “as is” in a Conda environment, using the latest version from the Biobakery Channel (since I am testing this before building a new container). No additional databases beyond what comes with the the Conda recipie are installed. So I am not sure if and how Humann3 has access to all the pathway mappings etc - it’s a little unclear from the documentation, to be honest. Cheers, Marc What would a simple series of command look like for this to work? ---
**Author:** ![Marc\_Hoeppner](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/marc_hoeppner/32/525_2.png) [@Marc\_Hoeppner](https://forum.biobakery.org/u/Marc_Hoeppner)\ **Post date:** [March 11, 2021, 12:30pm UTC](https://forum.biobakery.org/t/humann-3-0-and-bowtie-metaphlan-output/1049/5 "2021-03-11T12:30:53Z")
Hi, just a friendly bump - still stuck on this. ---
**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:** [March 11, 2021, 2:15pm UTC](https://forum.biobakery.org/t/humann-3-0-and-bowtie-metaphlan-output/1049/6 "2021-03-11T14:15:57Z")
HUMAnN will still need a metagenome or metatranscriptome (in e.g. FASTQ format) passed as input. Providing the MetaPhlAn taxonomic profile to HUMAnN is a shortcut: i.e. telling HUMAnN “assume these species are present” rather than working out who’s there yourself. The next step is to map the meta-ome against those species’ pangenomes, hence still needing that file as the primary input (`-i`).