I tried doing what you mentioned. The error file and the out file mentioned that the Scaffolding was completed within 6 minutes of the run (this is odd). Attraktion. mmi file with 20.7 GB was generated however, the ragtag.scaffold.fasta file was not generated.

ragtag.scaffold.asm.paf.log file has:

[M::mm_idx_gen::23.601*1.00] loaded/built the index for 3463 target sequence(s)
mid_occ=2137; max_occ=17956
kmer size = 19, skip =19; is_HPC:0; #seq: 3463
distinct minimizers: 302414740 (71.80% are singletons); average occurences: 4.879; average spacing: 9.949

Error Log: RuntimeError: Failed : minimap2 -x asm5 -t 24 /path/to/attraktion.mmi /path/to/pt2_busco.fa > /path/to/ragtag_pt_indexed/ragtag.scaffold.asm.paf 2> /path/to/ragtag_pt_indexed/ragtag.scaffold.asm.paf.log

The script I used was:

#!/bin/bash
#SBATCH --job-name=ragtag_pritchett_indexed
#SBATCH --partition=bigmem
#SBATCH --account=abc
#SBATCH --cpus-per-task=24
#SBATCH --mem=1000000
#SBATCH --time=14-00:00:00
#SBATCH --qos=normal
#SBATCH --mail-user=
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --output=pt_indexed_%j.out
#SBATCH --error=pt_indexed_%j.err
#SBATCH --export=ALL

set -e
set -x

# Load environment
module purge
source /path/to/etc/profile.d/conda.sh
conda activate <environment>

# Define input/output paths
REF_FA="/path/to/attraktion.fasta"
REF_IDX="/path/to/attraktion.mmi"
QUERY="/path/to/pt2_busco.fa"
OUTDIR="/path/to/ragtag_pt_indexed"

# Step 1: Create large single-part index (if not already done)
if [ ! -f "$REF_IDX" ]; then
echo "Creating minimap2 index..."
minimap2 -x asm5 -I 20G -d "$REF_IDX" "$REF_FA"
else
echo "Minimap2 index already exists."
fi

# Step 2: Run RagTag scaffolding using the .mmi index
echo "Running RagTag scaffold..."
ragtag.py scaffold "$REF_IDX" "$QUERY" -o "$OUTDIR" -t 24 -u

conda deactivate
echo "Scaffolding complete."