Is it possible that humann3 directly output bz2 file?

Hi Biobackery team,

Metaphlan3 is capable to re-run extremely fast by producing .bz2 file and humann3 is also based on methphlan3 for taxonomy profiling.
So I am wondering that if there is a option to tell humann3 to produce a .bz2 file among its temp files.

I tired --metaphlan-option " -t rel_ab --bowtie2out myfastq.bowtie2.bz2" but not worked.

Is there another way to do this?

Thank you in advance.


The temporary file from MetaPhlAn is saved under the HUMAnN temp folder for your sample (though it is probably not bz2 compressed there). You could use this file to rerun MetaPhlAn analyses very quickly. There is no equivalent highly reduced file for HUMAnN, in part because HUMAnN is interested in mapping results for all reads against any gene, whereas MetaPhlAn is mapping a subset of reads to a subset of genes (taxonomic markers).

1 Like

Thanks a lot, I got your idea