Humann3 pathway issue

Hi @franzosa,

I was trying to run humann3 on galaxy server with the command “humann --input demo.fastq -o output --threads 32 --metaphlan-options=”-t rel_ab --index mpa_v30_CHOCOPhlAn_201901 --bowtie2db /mnt/galaxyIndices/mpa_v30_chocophlan_201901" --nucleotide-database ‘/mnt/galaxyIndices/chocophlan’ --translated-alignment ‘diamond’ --protein-database ‘/mnt/galaxyIndices/uniref/’ --search-mode ‘uniref50’ --pathways ‘metacyc’ --annotation-gene-index 3 --evalue ‘1.0’ --memory-use minimum --prescreen-threshold ‘0.05’ --translated-subject-coverage-threshold ‘50.0’ --translated-query-coverage-threshold ‘90.0’ --xipe ‘off’ --minpath ‘on’ --gap-fill ‘on’ --output-format ‘tsv’

Here, I am not getting the expected number of output for pathway abundance and coverage.

I am not sure, what is going wrong in the command. I would highly appreciate your help for this.

Thanks,
Abhishek