The bioBakery help forum

Just one species in my output file

Hi there,

A ran an profiling analyisis with the next input:

/home/pavel/anaconda3/bin/metaphlan 88_B_S212_R1_001.fastq.gz,88_B_S212_R2_001.fastq.gz --bowtie2out metagenome.bowtie2.bz2 --nproc 8 --input_type fastq -o profiled_metagenome.txt

The result was very simple, but I know i have many kinds of archaeas in muy imput fastq:

#mpa_v30_CHOCOPhlAn_201901
#/home/pavel/anaconda3/bin/metaphlan 88_B_S212_R1_001.fastq.gz,88_B_S212_R2_001.fastq.gz --bowtie2out metagenome.bowtie2.bz2 --nproc 8 --input_type fastq -o profiled_metagenome.txt
#SampleID Metaphlan_Analysis
#clade_name NCBI_tax_id relative_abundance additional_species
k__Archaea 2157 100.0
k__Archaea|p__Euryarchaeota 2157|28890 100.0
k__Archaea|p__Euryarchaeota|c__Halobacteria 2157|28890|183963 100.0
k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales 2157|28890|183963|2235 100.0
k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales|f__Halobacteriaceae 2157|28890|183963|2235|2236 100.0
k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales|f__Halobacteriaceae|g__Halobacterium 2157|28890|183963|2235|2236|2239 100.0
k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales|f__Halobacteriaceae|g__Halobacterium|s__Halobacterium_salinarum 2157|28890|183963|2235|2236|2239|2242 100.0

Anybody knows the reason I just get one species in my output file?

Thanks.