Unexpected output (format)

[fbeghini]

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

@Afrojuju

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

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).