Metaphlan analysis show 100 % unknown

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