No mitochondrial genes after the run

[l1y1y]

My index and bam files are normal with mitochondrial genes, but the scTE runs just don't have mitochondrial genes, please help me to see if there is a problem with my scripts.

samtools idxstats possorted_genome_bam.bam | grep chrM
chrM 16569 16612227 0

samtools idxstats possorted_genome_bam.bam | grep chrM
chrM 16569 23620722 0

grep "chrM" /public/home/zzs000213/human_index/scte_index/hg38.exclusive.idx
Binary file /public/home/zzs000213/human_index/scte_index/hg38.exclusive.idx matches

#!/bin/bash
#SBATCH --job-name=scte
#SBATCH --partition=bingxing
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --array=1-2%2
#SBATCH --mem=110G
#SBATCH --output=scte_output_%A_%a.txt
#SBATCH --error=scte_error_%A_%a.txt

source /public/software/apps/anaconda3/5.2.0/etc/profile.d/conda.sh
conda activate scte

cd /public/home/zzs000213/data_yao/single-cell/Data/CleanData/output || { echo "erroe "; exit 1; }

index=$SLURM_ARRAY_TASK_ID

file=$(find . -type f -name "possorted_genome_bam.bam" | sed -n "${index}p")

sample_name=$(basename $(dirname $(dirname "$file")))

output_dir="$sample_name"
mkdir -p "$output_dir"

scTE -i "$file" -o "$output_dir" -x /public/home/zzs000213/human_index/scte_index/hg38.exclusive.idx -p 8

[l1y1y]

@jphe @oaxiom @carmarpe I would very much like your help, can you help me?

[l1y1y]

@jphe @oaxiom @carmarpe please help me, I really can't find the problem!