FileNotFoundError: [Errno 2] No such file or directory: 'output/bowtie2/metadata.yaml'

[bark9299]

I am trying to run the following command in the shogun conda environment: shogun align -a bowtie2 -i combined_seqs.fna -d /lfs/bark9299.ui/Sweden_shotgun_metagenomics/20240209_DNASeq_PE150/CLEAN_READS/clean_reads/output/bowtie2 -o /lfs/bark9299.ui/Sweden_shotgun_metagenomics/20240209_DNASeq_PE150/CLEAN_READS/clean_reads/output/shogun_output where the directory bowtie2 has the WoLr2 indexed database. I am getting an error about a metadata.yaml file and I see in your database creation section of the readme that i need this file but I am not using BURST, I am using bowtie2. How do I make the correct metadata.yaml file if I am only using bowtie2? This is not the same thing as the taxonomy file?

I'm just confused about formating the database part to use correctly with SHOGUN