for SAMPLE in 2 3 4 5 6; do
  # Input BAM files must be sorted by name
  INPUT_BAM="$SAMPLE-filtered-SOI-all-alignments.bam"
  OUTPUT_PATH="$SAMPLE-metaDMG-$LEVEL"
  OUTPUT_PREFIX="$SAMPLE"

  LEVEL=genus
  NAMES_DMP="/mounts/lovelace2/metadmg-data/names.dmp"
  NODES_DMP="/mounts/lovelace2/metadmg-data/nodes.dmp"
  ACC2TAX="/mounts/lovelace2/metadmg-data/nucl_gb.accession2taxid"
  THREADS=10

  mkdir $SAMPLE-metaDMG-$LEVEL

  echo "metaDMG-cpp lca \
    --names $NAMES_DMP \
    --nodes $NODES_DMP \
    --acc2tax $ACC2TAX \
    --sim_score_low 0.85 \
    --sim_score_high 1.0 \
    --how_many 100 \
    --fix_ncbi 0 \
    --lca_rank $LEVEL \
    --threads $THREADS \
    --bam $INPUT_BAM \
    --out_prefix $OUTPUT_PATH/$OUTPUT_PREFIX"

  echo "metaDMG-cpp dfit \
    $OUTPUT_PATH/$OUTPUT_PREFIX.bdamage.gz \
    --threads $THREADS \
    --names $NAMES_DMP \
    --nodes $NODES_DMP \
    --showfits 2 \
    --nopt 10 \
    --nbootstrap 20 \
    --doboot 1 \
    --seed 1234 \
    --lib ds \
    --out_prefix $OUTPUT_PATH/$OUTPUT_PREFIX"

  echo "metaDMG-cpp aggregate \
    $OUTPUT_PATH/$OUTPUT_PREFIX.bdamage.gz \
    --names $NAMES_DMP \
    --nodes $NODES_DMP \
    --lcastat $OUTPUT_PATH/$OUTPUT_PREFIX.stat.gz \
    --dfit $OUTPUT_PATH/$OUTPUT_PREFIX.dfit.gz \
    --out_prefix $OUTPUT_PATH/$OUTPUT_PREFIX.agg" 
done;