- I have installed HUMAnN2 from bioconda and downloaded respective Metaphlan data base (mpa_v20_m200), Chocophlan database (full_chocophlan_plus_viral.v0.1.1.tar.gz) and uniref90 database (uniref90_annotated.1.1.dmnd).
- I merged the paired end reads through flash.
- I run the command humann2 --input merged.fastq --output humann2_out.
-Though my sample is rice paddy soil sample (highly diverse), only 10 species were detected after the successful completion of Metaphlan run. Why ?
- Among them only two are selected for functional annotation. Why ?
- The command is running from last 24 hr, how much time it generally take to complete analysis.
- Am I doing something wrong or something is missing ?
Please suggest, what should I do ?