Can I use the option --bowtie2out (for StrainPhlan!) along HUMANn?

Microbial community profiling HUMAnN
1

Dear users,

I have HUMANn 3.8 installed and wanted to recover a taxonomic and functional profile with our samples. After I am looking at the StrainPhlan tutorial and I need to provide these options within metaphlan

metaphlan ${f} --input_type fastq -s sams/${bn}.sam.bz2 --bowtie2out bowtie2/${bn}.bowtie2.bz2 -o profiles/${bn}_profiled.tsv

I wonder if I can run HUMANn with these MetaPhlAn options so I can use StrainPhlan later on

humann --input /run/media/andrespara/HUMANN/N06.fastq.gz --output ./OUT/N06 --threads 6 --metaphlan-options "--bowtie2db /home/andrespara/andres/nowmetaphlan -s ./SAMS/N06.sam.bz2 --bowtie2out ./BOWTIE2/N06.bowtie2.bz2" --memory-use minimum --nucleotide-database "/home/andrespara/andres/chocophlan"

This worked partially since I got a SAMS folder an sam files but the BOWTIE2 folder is empty. An additional question would be "Can I use the bowtie files within the humann_temp folder to feed StrainPhlan?

Thanks

Best

Andrés

2

You can pass additional options to MetaPhlAn via HUMAnN using the --metaphlan-options flag. However, I find it’s often easier to just run MetaPhlAn outside of HUMAnN (using whatever parameters you’d like), and then pass the resulting taxonomic profile to HUMAnN via its --taxonomic-profile flag. It turns into a two-step process per sample, but it makes it a little easier to control each step.

3

Thanks for your help, I am now trying to run both HUMAn 4 and MetaPhlAn 4 I installed both software in the same environment and maybe that made it difficult to setup the databases (I got an error similar to Humann database errors (a short novel) - #3 by RbccBstn). I am currently re-downloading the metaphlan database to make it work but I wanted to thank you for this reply above.

Best

Andrès