以下のスクリプトを用意して実行しました。

#!/bin/bash
# 出力はmy-cohort-smoove.genotyped.vcf.gzとなる
# hg19/b37, hg38/b38のどちらかのproblematic regionをbed変数に格納する
# 今回はhg38なので，hg38の場合
reference_fasta="/home/inf/variant_call/tools/smoove/cram/GRCh38_full_analysis_set_plus_decoy_hla.fa"
bed="/home/inf/variant_call/tools/smoove/cram/exclude.cnvnator_100bp.GRCh38.20170403.bed"
# hg19の場合は以下のようにする
# reference_fasta="/home/inf/variant_call/tools/smoove/cram/hs37d5.fa"
# bed="/home/inf/variant_call/tools/smoove/cram/ceph18.b37.lumpy.exclude.2014-01-15.bed"
# CPUのコア数（ハイパースレッディング対応の場合はスレッド数）に応じて値を決める
threads=4

# Smooveコンテナのパス
smoove_container="/home/inf/variant_call/tools/smoove/cram/smoove.simg"

# デバッグ用出力
echo "Using reference fasta: ${reference_fasta}"
echo "Using exclusion bed: ${bed}"
echo "Using CRAM files: /home/inf/variant_call/tools/smoove/cram/*.cram"

# smooveの実行
singularity exec $smoove_container smoove call --removepr \
--name my-cohort \
--exclude ${bed} \
--fasta ${reference_fasta} \
--processes ${threads} \
--genotype \
/home/inf/variant_call/tools/smoove/cram/*.cram

すると以下のようなエラーが出ました。
inf@inf-PowerEdge-T110-II:~/variant_call/tools/smoove/cram$ ~/variant_call/tools/smoove/cram/run_smoove.sh
Using reference fasta: /home/inf/variant_call/tools/smoove/cram/GRCh38_full_analysis_set_plus_decoy_hla.fa
Using exclusion bed: /home/inf/variant_call/tools/smoove/cram/exclude.cnvnator_100bp.GRCh38.20170403.bed
Using CRAM files: /home/inf/variant_call/tools/smoove/cram/*.cram
[smoove] 2024/06/28 07:12:38 starting with version 0.2.8
[smoove] 2024/06/28 07:12:38 calculating bam stats for 4 bams
[smoove] 2024/06/28 07:12:56 done calculating bam stats
[smoove]: ([E]lumpy-filter) 2024/06/28 07:44:53 Failed to populate reference for id 111
[smoove]:([E]lumpy-filter) 2024/06/28 07:44:55 Failed to populate reference for id 150
[smoove]:([E]lumpy-filter) 2024/06/28 07:44:55 Failed to populate reference for id 168
[smoove]:([E]lumpy-filter) 2024/06/28 07:44:55 Failed to populate reference for id 168
[smoove]:([E]lumpy-filter) 2024/06/28 07:44:55 Failed to populate reference for id 168
[smoove]:([E]lumpy-filter) 2024/06/28 07:44:55 Failed to populate reference for id 168
以下同じようなエラーが続く
・・・
・・・
[smoove]:([E]lumpy-filter) 2024/06/28 07:46:03 [lumpy_filter] extracted splits and discordants from 635346592 total aligned reads
[smoove]:2024/06/28 07:46:16 finished process: lumpy-filter (set -eu; lumpy_filter -f /home/inf/variant_call/tools/smoove/cram/GRCh38_full_analysis_set_plus_deco) in user-time:32m11.907987s system-time:18.934444s
これを解決するための方法として何かアドバイス有りましたらご教授よろしくお願いいたします。