StrainPhlAn no clades found


I am using StrainPhlAn for the 1st time. When running it with --print_clades_only to find suitable clades (on 18 samples, but I’ve got more) I get an empty print_clades_only.tsv file with no clades. I’d be thankful for an explanation of what I’m doing wrong.

mkdir -p sams
mkdir -p bowtie2
mkdir -p profiles
for f in fastq/Ilany*
echo "Running MetaPhlAn on ${f}"
bn=$(basename ${f})
metaphlan ${f} --input_type fastq -s sams/${bn}.sam.bz2 --bowtie2out bowtie2/${bn}.bowtie2.bz2 -o profiles/${bn}_profiled.tsv --bowtie2db ~/Documents --nproc 8

mkdir -p consensus_markers -i sams/*.sam.bz2 -o consensus_markers -n 8 -d ~/Documents/mpa_vOct22_CHOCOPhlAnSGB_202212.pkl

strainphlan -s consensus_markers/*.pkl -o output --print_clades_only -d ~/Documents/mpa_vOct22_CHOCOPhlAnSGB_202212.pkl