Metaphla4 rel_ab_w_read_stats issue

Hi metaphlan author,

I used metaphlan4 (4.0.1) to generate profile. The following few lines are attached below. My issue is checking bacteria count (59839072). It is more than bowtie2 input reads (15148903). I also run the similar command using metaphlan 3.0.6. It doesn’t have this issue. I notice in another thread, someone claim there is issue to run using rel_ab_w_read_stats. Do you have a solution? Thanks a lot!

“#/opt/conda/bin/metaphlan results/metaphlan3/HND0022_un.fastq.bowtie2out.txt --input_type bowtie2out --nproc 8 --bowtie2db /data/wany/MGS_test/database/metaphlan4 -t rel_ab_w_read_stats --unclassified_estimation
#SampleID Metaphlan_Analysis
#estimated_reads_mapped_to_known_clades:59839072
#clade_name clade_taxid relative_abundance coverage estimated_number_of_reads_from_the_clade
UNCLASSIFIED -1 41.75627 - 0
k__Bacteria 2 58.24373 3.19643 59839072
k__Bacteria|p__Firmicutes 2|1239 20.53348 1.12688 16203915
k__Bacteria|p__Actinobacteria 2|201174 15.97619 0.87678 14740033
k__Bacteria|p__Proteobacteria 2|1224 11.54269 0.63347 10348415”

Hi @mentorwan
Thanks for reporting this issue. We will have a look at it and try to include a fix in the next version (4.0.3)

Hi @mentorwan
The new 4.0.3 version is now available in conda and should solve this issue

Thanks for updating. I will check.