# 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:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![Afrojuju](https://avatars.discourse-cdn.com/v4/letter/a/74df32/32.png) [@Afrojuju](https://forum.biobakery.org/u/Afrojuju)\
**Post date:** [July 1, 2020, 4:20pm UTC](https://forum.biobakery.org/t/unexpected-output-format/658/1 "2020-07-01T16:20:13Z")

</div>

Hello,

I’m using the latest version of MetaPhlAn3 (version 3.0.1 -\> 25 Jun 2020) and I’m getting an output that I am not sure that the format is correct or how to interpret interpret it

cmd:  
zcat sample.pair.1.fq.gz sample.pair.2.fq.gz | metaphlan --input\_type fastq -t rel\_ab --add\_viruses --nproc 8 --tax\_lev a --sample\_id\_key ‘#’ --no\_map -o met301\_output

It runs successfully but with the following warnings:

```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.
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.

```

output:

```auto
#mpa_v30_CHOCOPhlAn_201901
#/g/scb2/bork/mocat/software/metaphlan/3.0.1/metaphlan --input_type fastq -t rel_ab --add_viruses --nproc 8 --tax_lev a --sample_id_key # --no_map -o met301_output
##	Metaphlan_Analysis
#clade_name	NCBI_tax_id	relative_abundance	additional_species
k__Bacteria	2	98.5612
k__Archaea	2157	1.4388
k __Bacteria|p__ Bacteroidetes	2|976	86.06614
k __Bacteria|p__ Firmicutes	2|1239	7.13839
k __Bacteria|p__ Actinobacteria	2|201174	2.8684
k __Bacteria|p__ Proteobacteria	2|1224	2.48827
k __Archaea|p__ Euryarchaeota	2157|28890	1.4388
k __Bacteria|p__ Bacteroidetes|c__Bacteroidia	2|976|200643	86.06614
k __Bacteria|p__ Firmicutes|c__Bacilli	2|1239|91061	3.79753
k __Bacteria|p__ Firmicutes|c__Clostridia	2|1239|186801	2.84848
k __Bacteria|p__ Actinobacteria|c__Actinobacteria	2|201174|1760	2.55458
.
.
.
k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Odoribacteraceae|g__ Butyricimonas	2|976|200643|171549|1853231|574697	0.05371
k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Bacteroidaceae|g__ Bacteroides|s __Bacteroides_uniformis	2|976|200643|171549|815|816|820	30.08586	k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Bacteroidaceae|g __Bacteroides|s__ Bacteroides_sp_D20,k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Bacteroidaceae|g__ Bacteroides|s __Bacteroides_sp_AR29,k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Bacteroidaceae|g __Bacteroides|s__ Bacteroides_uniformis_CAG_3,k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Bacteroidaceae|g__ Bacteroides|s__Bacteroides_sp_4_1_36
k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Bacteroidaceae|g__ Bacteroides|s __Bacteroides_caccae	2|976|200643|171549|815|816|47678	21.5374	k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Bacteroidaceae|g __Bacteroides|s__ Bacteroides_sp_43_46
k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Bacteroidaceae|g__ Bacteroides|s __Bacteroides_dorei	2|976|200643|171549|815|816|357276	7.57107	k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Bacteroidaceae|g __Bacteroides|s__ Bacteroides_sp_3_1_33FAA,k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Bacteroidaceae|g__ Bacteroides|s__Bacteroides_sp_9_1_42FAA
k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Tannerellaceae|g__ Parabacteroides|s __Parabacteroides_distasonis	2|976|200643|171549|2005525|375288|823	7.28879	k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Tannerellaceae|g __Parabacteroides|s__ Parabacteroides_sp_20_3,k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Tannerellaceae|g__ Parabacteroides|s __Parabacteroides_sp_2_1_7,k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Porphyromonadaceae|g __Porphyromonas|s__ Porphyromonas_sp_31_2,k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Tannerellaceae|g__ Parabacteroides|s __Parabacteroides_sp_AT13,k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Bacteroidaceae|g __Bacteroides|s__ Bacteroides_sp_2_1_33B,k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Tannerellaceae|g__ Parabacteroides|s __Parabacteroides_sp_D25,k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Tannerellaceae|g __Parabacteroides|s__ Parabacteroides_sp_AM17_47,k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Tannerellaceae|g__ Parabacteroides|s __Parabacteroides_sp_D13,k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Tannerellaceae|g __Parabacteroides|s__ Parabacteroides_sp_CT06,k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Tannerellaceae|g__ Parabacteroides|s __Parabacteroides_sp_D26,k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Tannerellaceae|g __Parabacteroides|s__ Parabacteroides_sp_AM25_14,k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Bacteroidaceae|g__ Bacteroides|s __Bacteroides_sp_3_1_19,k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Tannerellaceae|g __Parabacteroides|s__ Parabacteroides_sp_CAG_2
k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Rikenellaceae|g__ Alistipes|s __Alistipes_putredinis	2|976|200643|171549|171550|239759|28117	6.93637	k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Rikenellaceae|g __Alistipes|s__ Alistipes_sp,k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Rikenellaceae|g__ Alistipes|s__Alistipes_putredinis_CAG_67
k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_faecium	2|1239|91061|186826|81852|1350|1352	3.79753	k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC034B11,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC056C08,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_10F3_DIV0382,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC060D07,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC060E05,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC069A01,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_GMD5E,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_GMD1E,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC077E07,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC34G12,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC072F02,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_3G1_DIV0629,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC063C12,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC067C01,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC076D08,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC063D12,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC077E04,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC065H03,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC070F12,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC063H10,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC073E07,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC074F07,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HPCN18,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC035B04,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC058D07,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC072F07,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC035C10,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC061C05,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC055G03,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC076E04,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC073E08,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC072D11,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC072G01,k __Bacteria|p__ Firmicutes|c __Bacilli|o__ Lactobacillales|f __Enterococcaceae|g__ Enterococcus|s __Enterococcus_sp_HMSC060D09,k__ Bacteria|p __Firmicutes|c__ Bacilli|o __Lactobacillales|f__ Enterococcaceae|g __Enterococcus|s__ Enterococcus_sp_HMSC065H12
k __Bacteria|p__ Bacteroidetes|c __Bacteroidia|o__ Bacteroidales|f __Odoribacteraceae|g__ Odoribacter|s __Odoribacter_splanchnicus	2|976|200643|171549|1853231|283168|28118	2.79578	k__ Bacteria|p __Bacteroidetes|c__ Bacteroidia|o __Bacteroidales|f__ Odoribacteraceae|g __Odoribacter|s__ Odoribacter_splanchnicus_CAG_14
k __Bacteria|p__ Firmicutes|c __Clostridia|o__ Clostridiales|f __Ruminococcaceae|g__ Ruminococcus|s __Ruminococcus_bromii	2|1239|186801|186802|541000|1263|40518	2.71565	k__ Bacteria|p __Firmicutes|c__ Clostridia|o __Clostridiales|f__ Ruminococcaceae|g __Ruminococcus|s__ Ruminococcus_sp,k __Bacteria|p__ Firmicutes|c __Clostridia|o__ Clostridiales|f __Ruminococcaceae|g__ Ruminococcus|s __Ruminococcus_sp_AM28_29LB,k__ Bacteria|p __Firmicutes|c__ Clostridia|o __Clostridiales|f__ Ruminococcaceae|g __Ruminococcus|s__ Ruminococcus_sp_AF43_11,k __Bacteria|p__ Firmicutes|c __Clostridia|o__ Clostridiales|f __Ruminococcaceae|g__ Ruminococcus|s __Ruminococcus_sp_AM31_32,k__ Bacteria|p __Firmicutes|c__ Clostridia|o __Clostridiales|f__ Ruminococcaceae|g __Ruminococcus|s__ Ruminococcus_sp_AF37_3AC,k __Bacteria|p__ Firmicutes|c __Clostridia|o__ Clostridiales|f __Ruminococcaceae|g__ Ruminococcus|s __Ruminococcus_sp_AM36_18,k__ Bacteria|p __Firmicutes|c__ Clostridia|o __Clostridiales|f__ Ruminococcaceae|g __Ruminococcus|s__ Ruminococcus_sp_AF42_10,k __Bacteria|p__ Firmicutes|c __Clostridia|o__ Clostridiales|f __Ruminococcaceae|g__ Ruminococcus|s __Ruminococcus_sp_AF17_11,k__ Bacteria|p __Firmicutes|c__ Clostridia|o __Clostridiales|f__ Ruminococcaceae|g __Ruminococcus|s__ Ruminococcus_sp_CAG_108,k __Bacteria|p__ Firmicutes|c __Clostridia|o__ Clostridiales|f __Ruminococcaceae|g__ Ruminococcus|s __Ruminococcus_sp_AM34_10LB,k__ Bacteria|p __Firmicutes|c__ Clostridia|o __Clostridiales|f__ Ruminococcaceae|g __Ruminococcus|s__ Ruminococcus_sp_TF12_19AC,k __Bacteria|p__ Firmicutes|c __Clostridia|o__ Clostridiales|f __Ruminococcaceae|g__ Ruminococcus|s__Ruminococcus_sp_AF16_40

```

Can you please clarify that the output is what is expected and if yes, how is it to be interpreted

---

<div class="post-metadata">

**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")

</div>

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`).

---

<div class="post-metadata">

**Author:** ![Afrojuju](https://avatars.discourse-cdn.com/v4/letter/a/74df32/32.png) [@Afrojuju](https://forum.biobakery.org/u/Afrojuju)\
**Post date:** [July 2, 2020, 10:06am UTC](https://forum.biobakery.org/t/unexpected-output-format/658/3 "2020-07-02T10:06:36Z")

</div>

Thank you for the quick reply.

Can you please advice on how to interpret the new format in comparison to the old metaphlan2 format

Best  
W

---

<div class="post-metadata">

**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, 10:32am UTC](https://forum.biobakery.org/t/unexpected-output-format/658/4 "2020-07-02T10:32:21Z")

</div>

The first two columns are linked to the taxonomy of the clade, the first one is the seven-level taxonomy with the clade name, the second one is the same seven-level taxonomy but instead the clade name, each level is the associated NCBI taxonomy ID.  
Relative abundance of the clade is present in the third column.  
The latest column lists the alternative" species name as I described you in the previous post.

You can see that are present more header lines: first one is the name and version of the database used for the profiling. We introduced also the command line used to perform the analysis.

---

<div class="post-metadata">

**Author:** ![Afrojuju](https://avatars.discourse-cdn.com/v4/letter/a/74df32/32.png) [@Afrojuju](https://forum.biobakery.org/u/Afrojuju)\
**Post date:** [July 2, 2020, 10:58am UTC](https://forum.biobakery.org/t/unexpected-output-format/658/5 "2020-07-02T10:58:20Z")

</div>

That helps greatly.

Thank you again for the time