# Unexpected output (format)

**URL:** <https://forum.biobakery.org/t/unexpected-output-format/658>\
**Category:** MetaPhlAn\
**Created:** [July 1, 2020, 4:20pm UTC](https://forum.biobakery.org/t/unexpected-output-format/658 "2020-07-01T16:20:13Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [July 2, 2020, 8:03am UTC](https://forum.biobakery.org/t/unexpected-output-format/658/2 "2020-07-02T08:03:42Z")

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The command used and the output obtained are OK, this is the new format introduced in version 3.

> [@Afrojuju](#):
>
> ```auto
> Use of uninitialized value $bt2_args[2] in join or string at /g/scb2/bork/mocat/software/metaphlan/3.0.1/bowtie2 line 423.
> Use of uninitialized value $bt2_args[3] in join or string at /g/scb2/bork/mocat/software/metaphlan/3.0.1/bowtie2 line 423.
> Use of uninitialized value $_[2] in string eq at /g/scb2/bork/mocat/software/metaphlan/3.0.1/bowtie2 line 360.
> Use of uninitialized value $_[3] in string eq at /g/scb2/bork/mocat/software/metaphlan/3.0.1/bowtie2 line 360.
> Use of uninitialized value in exists at /g/scb2/bork/mocat/software/metaphlan/3.0.1/bowtie2 line 81.
> Use of uninitialized value in exists at /g/scb2/bork/mocat/software/metaphlan/3.0.1/bowtie2 line 81.
> Use of uninitialized value $bt2_args[2] in join or string at /g/scb2/bork/mocat/software/metaphlan/3.0.1/bowtie2 line 459.
> Use of uninitialized value $bt2_args[3] in join or string at /g/scb2/bork/mocat/software/metaphlan/3.0.1/bowtie2 line 459.
> 
> ```

These warnings are not affecting the MetaPhlAn run, they come from bowtie2, the latest version available on bioconda has some issues.

> [@Afrojuju](#):
>
> ```auto
> WARNING: The metagenome profile contains clades that represent multiple species merged into a single representant.
> An additional column listing the merged species is added to the MetaPhlAn output.
> 
> ```

These are from MetaPhlAn, they just inform you that some species found can have “alternative” taxonomies (the list of species in the `additional_species` column). All the species listed under `additional_species` are not represented by any markers but they were found to be \<5% ANI distant from the “reference” species (`clade_name`).

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