# Metaphlan analysis show 100 % unknown

**URL:** <https://forum.biobakery.org/t/metaphlan-analysis-show-100-unknown/3762>\
**Category:** MetaPhlAn\
**Created:** [June 24, 2022, 1:52am UTC](https://forum.biobakery.org/t/metaphlan-analysis-show-100-unknown/3762 "2022-06-24T01:52:29Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Bakku](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/bakku/32/1516_2.png) [@Bakku](https://forum.biobakery.org/u/Bakku)\
**Post date:** [June 24, 2022, 1:52am UTC](https://forum.biobakery.org/t/metaphlan-analysis-show-100-unknown/3762/1 "2022-06-24T01:52:29Z")

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Hi, I am new to use Metaphlan,

I was able to successfully install the tool, but when I use my fastq files it give 100% unclassified.  
You can see below:

Command used:

sudo metaphlan E1\_R1\_001.fastq,E1\_R2\_001.fastq --bowtie2out E1\_R12.bowtie2.bz2 --nproc 5 --input\_type fastq --unknown\_estimation -o E1\_R12\_profile\_test2.txt

* * *

## #mpa\_v30\_CHOCOPhlAn\_201901 #/usr/bin/metaphlan E1\_R1\_001.fastq,E1\_R2\_001.fastq --bowtie2out E1\_R12.bowtie2.bz2 --nproc 5 --input\_type fastq --unknown\_estimation -o E1\_R12\_profile\_test2.txt #SampleID Metaphlan\_Analysis #clade\_name NCBI\_tax\_id relative\_abundance additional\_species UNKNOWN -1 100.0

I also tried using the chimera fasta file from the metagenomics data. However, I got the same result.

code: sudo metaphlan Euglena-1.fasta --input\_type fasta -o E1\_profile.txt

#mpa\_v30\_CHOCOPhlAn\_201901  
#/usr/bin/metaphlan Euglena-1.fasta --input\_type fasta -o @@@E1\_profile.txt  
#SampleID Metaphlan\_Analysis  
#clade\_name NCBI\_tax\_id relative\_abundance additional\_species  
UNKNOWN -1 100.0

* * *

I tried running metaphlan on SRS014472-Buccal\_mucosa.fasta.gz file and I was able to see result as shown below:

* * *

## #mpa\_v30\_CHOCOPhlAn\_201901 #/usr/bin/metaphlan SRS014476-Supragingival\_plaque.fasta.gz --input\_type fasta #SampleID Metaphlan\_Analysis #clade\_name NCBI\_tax\_id relative\_abundance additional\_species k\_\_Bacteria 2 100.0 k\_\_Bacteria|p\_\_Actinobacteria 2|201174 100.0 k\_\_Bacteria|p\_\_Actinobacteria|c\_\_Actinobacteria 2|201174|1760 100.0 k\_\_Bacteria|p\_\_Actinobacteria|c\_\_Actinobacteria|o\_\_Corynebacteriales 2|201174|1760|85007 66.19688 …etc

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<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [December 19, 2022, 4:40pm UTC](https://forum.biobakery.org/t/metaphlan-analysis-show-100-unknown/3762/2 "2022-12-19T16:40:47Z")

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Hi @Bakku  
Can I ask which type of environment are you trying to analyse? For some really uncharacterized environments that result could be partially expected