-t rel_ab_w_read_stats output error

Microbial community profiling MetaPhlAn
1

Hi,

I am running metaphlan 4 with the -t rel_ab_w_read_stats flag because I am interested in the absolute abundance.
This is the command I run:metaphlan ${base}_R1.fastq,${base}_R2.fastq --input_type fastq --bowtie2out ${base}.bowtie2.bz2 --bowtie2db /db --nproc 10 -t rel_ab_w_read_stats -o ${base}_profile.txt

However, for some of the taxa I found an incomplete/complete clade_taxid and for those I have a relative abundance value and no info on the coverage and read count per clade. instead there is “-” (see screenshot for example).

Please can you explain why I do not have information for these particular taxa even though they look to be very high in relative abundance?

Screenshot 2022-12-09 at 14 55 29

Thank you in advance for your help!

2

Hi @MatteoBuffoni
We had fixed the problem in the latest 4.0.3 version

3

Hi Aitor,

Thanks for the reply. However, we’re looking for the Docker container for this version on your official Dockerhub channel and cannot find it (yet). Would it be possible for you to release a Docker container for this 4.0.3 version?

4

Hi @MatteoBuffoni
For MetaPhlAn 4, we decided just to support the conda and pip installations until all the other biobakery tools are upgraded to version 4. Sorry for the inconvenience