Humann3 --metaphlan-options error

Microbial community profiling HUMAnN
1

Hello everyone,

I am running humann3 via a nextflow process when I execute the following command it works without any issues:

   humann3 \\
        ${args2} \\
        --input ${reads[0]} \\
        --output . \\
        --output-basename ${prefix} \\
        --nucleotide-database \$CHOCO  \\
        --protein-database \$UNIREF \\
        --threads ${task.cpus} \\
        --o-log ${prefix}.log \\
        --metaphlan-options "--bowtie2db ${metaphlan_index} --offline -t rel_ab_w_read_stats"

But once I add another argument to the --metaphlan-options such as --metaphlan-options "--bowtie2db ${metaphlan_index} --offline -t rel_ab_w_read_stats --stat_q 0.1 --profile_vsc", bowtie2 throws an error unrecognized argument --threads. At first I thought it was a scoping issue, but the original command works fine with only the -t flag.

The metaphlan command looks fine where --nproc is used, it seems that there is a leak from humann to the bowtie2, looks more like a issue in the script.

I run the code from the docker image biobakery/humann:latest, with versions; metaphlan=4.1.0, humann=3.9 and bowtie2=2.2.3.

I hope to hear from you.