[Issue] --nreads parameter when running MetaPhlAn using SAM files as input

Microbial community profiling MetaPhlAn
1

Hello, experts.
I am trying to use MetaPhlAn v. 4.0.6 (1 Mar 2023) to annotate taxonomy for metagenomic dataset.
(I used input data for merged fastq after removed host information.)
I followed the tutorial in the order. However, some issues occured in
“metaphlan metagenome.sam --input_type sam -o profiled_metagenome.txt” this process.

“Please provide the size of the metagenome using the --nreads parameter when running MetaPhlAn using SAM files as input
Exiting…”

Could you please give me some advice to solve this problem?
I used “mpa_vOct22_CHOCOPhlAnSGB_202212” this database.

Many thanks

2

I am getting the same error using the same metaphlan and database version. Did you were able to resolve this issue?
many thanks

3

Hi all,
When providing SAM file as input for metaphlan, it is mandatory to provide the original number of reads in the FASTq file for the normalization metaphlan does inside