Install and running Humann for the first time

Microbial community profiling HUMAnN
1

I have installed humann and metaphlan via pip. $human_test and $metaphlan --version OK, then I install human database via manual

when I using test sample,
$humann --input demo.fastq.gz --output demo_fastq
it got metaphlan database error, please help,

thanks so much!

2

I solved this, the important thing is make Bowtie2 and Diamond version correct, Humann use many other software. Hopefully we can have step by step manual for all setups

Also Minpath, I turned minpath off, hopefully not inflect the results

3

Turning off MinPath just means that HUMAnN will quantify all pathways. MinPath will otherwise try to quantify just a minimal subset of pathways that explain the detected reactions.

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