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

4

Dear all,

I was trying to run the pipeline using first metaphlan and then humann 4 alpha.
I installed diamond and also provided the route to the databases with humann_config

As per the documentation I tried the following:

# 001
metaphlan RAW/SRR14076335_1.fastq.gz --input_type fastq -s SAMS/SRR14076335.sam.bz2 --bowtie2out BOWTIE2/SRR14076335.bowtie2.bz2 -o BUGS/SRR14076335_profile.tsv --add_viruses --unclassified_estimation --index mpa_vOct22_CHOCOPhlAnSGB_202403 --bowtie2db ./CHOCO/mpa_vOct22_CHOCOPhlAnSGB_202403
# 002
bzip2 -d ./SAMS/SRR*
# 003
humann --input ./UNCOMPRESS/SRR14076335.sam --output ./FromSAMS/SRR14076335 --metaphlan-options "--bowtie2db ./CHOCO --index mpa_vOct22_CHOCOPhlAnSGB_202403" --nucleotide-database "./HUMANn/chocophlan" --threads 22

I haven’t exhaustively searched older threads but is there anything wrong with the procedure above? Or is there an alternate way to pass the metaphlan output to humann?
Thanks for the help,
Best,

Andrés

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