根据这些参考脚本内容”#!/bin/bash
################################ START OF YAHS
SCAFFOLDING TEST ################################
#### download the test data
## test is either "LYZE01" or "CHM13"
test="LYZE01"
#test="CHM13"
wget https://zenodo.org/record/7079219/files/${test}.contigs.fasta.gz
wget https://zenodo.org/record/7079219/files/${test}.contigs.fasta.gz.fai
wget https://zenodo.org/record/7079219/files/${test}.hic.qn.bam
out="test_out"
outdir="."
contigs="${test}.contigs.fasta.gz" # need to be indexed, i.e., ${test}.contigs.fasta.gz.fai is presented
hicaln="${test}.hic.qn.bam" # could be .bed, .bam or .bin file
#### run yahs
scaffolding
../yahs -o ${outdir}/${out} ${contigs} ${hicaln} || exit 1
## LYZE01 is a very small genome,
## better result when running YaHS with option "-r 1000,2000,5000,10000,20000,50000,100000,200000,500000"
#../yahs -r 1000,2000,5000,10000,20000,50000,100000,200000,500000 -o ${outdir}/${out} ${contigs} ${hicaln} || exit 1
################################# END OF YAHS
SCAFFOLDING TEST #################################
#### change doplot to 1 if you want to generate hic contact maps
## you also need to set the path of juicer_tools, pretext_map, pretext_snapshot, and samtools
doplot=0
if [ ${doplot} -eq 0 ]; then exit 0; fi
## need juicer_tools/pretextmap and samtools if want to do hic plot
## juicer_tools: https://github.com/aidenlab/juicer/wiki/Download
## PretextMap: https://github.com/wtsi-hpag/PretextMap
## PretexSnapshot: https://github.com/wtsi-hpag/PretextSnapshot
## samtools: https://github.com/samtools/samtools
## please adjust the path to juicer_tools and samtools
## here we use 12 CPUs and 32Gb memory for juicer_tools pre - adjust it according to your device
## see more information for juicer tools https://github.com/aidenlab/juicer/wiki/Juicer-Tools-Quick-Start
## output file will be ${outdir}/${out}.hic
## the output hic file could be viewed with JuiceBox https://github.com/aidenlab/Juicebox
#juicer_tools="java -Xmx32G -jar /bin/juicer_tools_1.22.01.jar pre --threads 12"
## v1.9.9 seems much faster than v1.22.01
juicer_tools="java -Xmx32G -jar /bin/juicer_tools.1.9.9_jcuda.0.8.jar pre"
pretext_map="/bin/PretextMap"
pretext_snapshot="/bin/PretextSnapshot"
samtools="/bin/samtools"
#### this is to generate input file for juicer_tools - non-assembly mode or for PretextMap
## here we use 8 CPUs and 32Gb memory for sorting - adjust it according to your device
(../juicer pre ${outdir}/${out}.bin ${outdir}/${out}_scaffolds_final.agp ${contigs}.fai 2>${outdir}/tmp_juicer_pre.log | LC_ALL=C sort -k2,2d -k6,6d -T ${outdir} --parallel=8 -S32G | awk 'NF' > ${outdir}/alignments_sorted.txt.part) && (mv ${outdir}/alignments_sorted.txt.part ${outdir}/alignments_sorted.txt)
## prepare chromosome size file from samtools index file
# ${samtools} faidx ${outdir}/${out}_scaffolds_final.fa
# cut -f1-2 ${outdir}/${out}_scaffolds_final.fa.fai >${outdir}/${out}_scaffolds_final.chrom.sizes
## another way to prepare chromosome size file
## this is an easier way especially when we have >2G scaffolds which need scaling
cat ${outdir}/tmp_juicer_pre.log | grep "PRE_C_SIZE" | cut -d' ' -f2- >${outdir}/${out}_scaffolds_final.chrom.sizes
## do juicer hic map
(${juicer_tools} ${outdir}/alignments_sorted.txt ${outdir}/${out}.hic.part ${outdir}/${out}_scaffolds_final.chrom.sizes) && (mv ${outdir}/${out}.hic.part ${outdir}/${out}.hic)
## do Pretext hic map
(awk 'BEGIN{print "## pairs format v1.0"} {print "#chromsize:\t"$1"\t"$2} END {print "#columns:\treadID\tchr1\tpos1\tchr2\tpos2\tstrand1\tstrand2"}' ${outdir}/${out}_scaffolds_final.chrom.sizes; awk '{print ".\t"$2"\t"$3"\t"$6"\t"$7"\t.\t."}' alignments_sorted.txt) | ${pretext_map} -o ${outdir}/${out}.pretext
# and a pretext snapshot
${pretext_snapshot} -m ${outdir}/${out}.pretext --sequences "=full" -o ${outdir}
#### this is to generate input file for juicer_tools - assembly (JBAT) mode (-a)
../juicer pre -a -o ${outdir}/${out}_JBAT ${outdir}/${out}.bin ${outdir}/${out}_scaffolds_final.agp ${contigs}.fai 2>${outdir}/tmp_juicer_pre_JBAT.log
cat ${outdir}/tmp_juicer_pre_JBAT.log | grep "PRE_C_SIZE" | cut -d' ' -f2- >${outdir}/${out}_JBAT.chrom.sizes
(${juicer_tools} ${outdir}/${out}_JBAT.txt ${outdir}/${out}_JBAT.hic.part ${outdir}/${out}_JBAT.chrom.sizes) && (mv ${outdir}/${out}_JBAT.hic.part ${outdir}/${out}_JBAT.hic)
#### this is to generate final genome assembly file after manual curation with JuiceBox (JBAT)
## the output assembly file after curation is ${outdir}/${out}_JBAT.review.assembly
## the final output is ${outdir}/${out}_JBAT.FINAL.agp and ${outdir}/${out}_JBAT.FINAL.fa
# ../juicer post -o ${outdir}/${out}_JBAT ${outdir}/${out}_JBAT.review.assembly ${outdir}/${out}_JBAT.liftover.agp ${contigs}“#!/bin/bash
################################ START OF YAHS
SCAFFOLDING TEST ################################
#### download the test data
## test is either "LYZE01" or "CHM13"
test="LYZE01"
#test="CHM13"
wget https://zenodo.org/record/7079219/files/${test}.contigs.fasta.gz
wget https://zenodo.org/record/7079219/files/${test}.contigs.fasta.gz.fai
wget https://zenodo.org/record/7079219/files/${test}.hic.qn.bam
out="test_out"
outdir="."
contigs="${test}.contigs.fasta.gz" # need to be indexed, i.e., ${test}.contigs.fasta.gz.fai is presented
hicaln="${test}.hic.qn.bam" # could be .bed, .bam or .bin file
#### run yahs
scaffolding
../yahs -o ${outdir}/${out} ${contigs} ${hicaln} || exit 1
## LYZE01 is a very small genome,
## better result when running YaHS with option "-r 1000,2000,5000,10000,20000,50000,100000,200000,500000"
#../yahs -r 1000,2000,5000,10000,20000,50000,100000,200000,500000 -o ${outdir}/${out} ${contigs} ${hicaln} || exit 1
################################# END OF YAHS
SCAFFOLDING TEST #################################
#### change doplot to 1 if you want to generate hic contact maps
## you also need to set the path of juicer_tools, pretext_map, pretext_snapshot, and samtools
doplot=0
if [ ${doplot} -eq 0 ]; then exit 0; fi
## need juicer_tools/pretextmap and samtools if want to do hic plot
## juicer_tools: https://github.com/aidenlab/juicer/wiki/Download
## PretextMap: https://github.com/wtsi-hpag/PretextMap
## PretexSnapshot: https://github.com/wtsi-hpag/PretextSnapshot
## samtools: https://github.com/samtools/samtools
## please adjust the path to juicer_tools and samtools
## here we use 12 CPUs and 32Gb memory for juicer_tools pre - adjust it according to your device
## see more information for juicer tools https://github.com/aidenlab/juicer/wiki/Juicer-Tools-Quick-Start
## output file will be ${outdir}/${out}.hic
## the output hic file could be viewed with JuiceBox https://github.com/aidenlab/Juicebox
#juicer_tools="java -Xmx32G -jar /bin/juicer_tools_1.22.01.jar pre --threads 12"
## v1.9.9 seems much faster than v1.22.01
juicer_tools="java -Xmx32G -jar /bin/juicer_tools.1.9.9_jcuda.0.8.jar pre"
pretext_map="/bin/PretextMap"
pretext_snapshot="/bin/PretextSnapshot"
samtools="/bin/samtools"
#### this is to generate input file for juicer_tools - non-assembly mode or for PretextMap
## here we use 8 CPUs and 32Gb memory for sorting - adjust it according to your device
(../juicer pre ${outdir}/${out}.bin ${outdir}/${out}_scaffolds_final.agp ${contigs}.fai 2>${outdir}/tmp_juicer_pre.log | LC_ALL=C sort -k2,2d -k6,6d -T ${outdir} --parallel=8 -S32G | awk 'NF' > ${outdir}/alignments_sorted.txt.part) && (mv ${outdir}/alignments_sorted.txt.part ${outdir}/alignments_sorted.txt)
## prepare chromosome size file from samtools index file
# ${samtools} faidx ${outdir}/${out}_scaffolds_final.fa
# cut -f1-2 ${outdir}/${out}_scaffolds_final.fa.fai >${outdir}/${out}_scaffolds_final.chrom.sizes
## another way to prepare chromosome size file
## this is an easier way especially when we have >2G scaffolds which need scaling
cat ${outdir}/tmp_juicer_pre.log | grep "PRE_C_SIZE" | cut -d' ' -f2- >${outdir}/${out}_scaffolds_final.chrom.sizes
## do juicer hic map
(${juicer_tools} ${outdir}/alignments_sorted.txt ${outdir}/${out}.hic.part ${outdir}/${out}_scaffolds_final.chrom.sizes) && (mv ${outdir}/${out}.hic.part ${outdir}/${out}.hic)
## do Pretext hic map
(awk 'BEGIN{print "## pairs format v1.0"} {print "#chromsize:\t"$1"\t"$2} END {print "#columns:\treadID\tchr1\tpos1\tchr2\tpos2\tstrand1\tstrand2"}' ${outdir}/${out}_scaffolds_final.chrom.sizes; awk '{print ".\t"$2"\t"$3"\t"$6"\t"$7"\t.\t."}' alignments_sorted.txt) | ${pretext_map} -o ${outdir}/${out}.pretext
# and a pretext snapshot
${pretext_snapshot} -m ${outdir}/${out}.pretext --sequences "=full" -o ${outdir}
#### this is to generate input file for juicer_tools - assembly (JBAT) mode (-a)
../juicer pre -a -o ${outdir}/${out}_JBAT ${outdir}/${out}.bin ${outdir}/${out}_scaffolds_final.agp ${contigs}.fai 2>${outdir}/tmp_juicer_pre_JBAT.log
cat ${outdir}/tmp_juicer_pre_JBAT.log | grep "PRE_C_SIZE" | cut -d' ' -f2- >${outdir}/${out}_JBAT.chrom.sizes
(${juicer_tools} ${outdir}/${out}_JBAT.txt ${outdir}/${out}_JBAT.hic.part ${outdir}/${out}_JBAT.chrom.sizes) && (mv ${outdir}/${out}_JBAT.hic.part ${outdir}/${out}_JBAT.hic)
#### this is to generate final genome assembly file after manual curation with JuiceBox (JBAT)
## the output assembly file after curation is ${outdir}/${out}_JBAT.review.assembly
## the final output is ${outdir}/${out}_JBAT.FINAL.agp and ${outdir}/${out}_JBAT.FINAL.fa
# ../juicer post -o ${outdir}/${out}_JBAT ${outdir}/${out}_JBAT.review.assembly ${outdir}/${out}_JBAT.liftover.agp ${contigs}”重新调整上面对话中的脚本“#!/bin/bash
#SBATCH -p amd_256
#SBATCH -N 1
#SBATCH -n 32
#SBATCH -t 96:00:00
#SBATCH --mem=256G
#SBATCH -J hic_chromap
#SBATCH -o /public1/home/scb3201/rawdata/Hic/logs/%j_chromap_out.log
#SBATCH -e /public1/home/scb3201/rawdata/Hic/logs/%j_chromap_err.log
##########################################################
# 1. 环境设置与路径定义
##########################################################
echo "[INFO] 开始Chromap Hi-C分析流程... $(date)"
# 记录开始时间
START_TIME=$(date +%s)
# 激活Conda环境
source ~/.bashrc
conda activate Hic || {
echo "[ERROR] Hic环境激活失败! $(date)"
exit 1
}
# 核心路径
BASE_DIR="/public1/home/scb3201/rawdata/Hic"
RESULTS_DIR="/public1/home/scb3201/results/genome/Hic"
REF_GENOME="/public1/home/scb3201/results/genome/Medaka/genome.nextpolish.medaka.fasta"
READ1="${BASE_DIR}/reads/hic_R1.fastq.gz"
READ2="${BASE_DIR}/reads/hic_R2.fastq.gz"
# 子目录
ALIGN_DIR="${RESULTS_DIR}/alignment"
SCAFFOLD_DIR="${RESULTS_DIR}/scaffold"
JUICEBOX_DIR="${RESULTS_DIR}/juicebox"
LOG_DIR="${BASE_DIR}/logs"
TMP_DIR="${BASE_DIR}/tmp"
# 创建目录
mkdir -p ${ALIGN_DIR} ${SCAFFOLD_DIR} ${JUICEBOX_DIR} ${LOG_DIR} ${TMP_DIR}
# 设置临时目录
export TMPDIR=${TMP_DIR}
export _JAVA_OPTIONS="-Xmx200G -Xms64G"
# 获取任务ID用于日志命名
JOB_ID=${SLURM_JOB_ID:-manual_$(date +%s)}
##########################################################
# 2. 参考基因组准备
##########################################################
echo "[STEP] 准备参考基因组... $(date)"
# 函数：检查步骤执行状态
check_status() {
if [ $? -ne 0 ]; then
echo "[ERROR] $1 失败! $(date)"
exit 1
fi
}
# 生成Chromap索引
if [[ ! -f ${REF_GENOME}.chromap.idx ]]; then
echo "[INFO] 创建Chromap索引..."
chromap --preset hic -i -r ${REF_GENOME} -o ${REF_GENOME}.chromap.idx 2> ${LOG_DIR}/chromap_index_${JOB_ID}.log
check_status "Chromap索引创建"
else
echo "[INFO] 已存在Chromap索引，跳过创建"
fi
# 生成染色体长度文件
if [[ ! -f ${REF_GENOME}.fai ]]; then
echo "[INFO] 创建参考基因组索引..."
samtools faidx ${REF_GENOME} 2> ${LOG_DIR}/samtools_faidx_${JOB_ID}.log
check_status "参考基因组索引创建"
else
echo "[INFO] 已存在参考基因组索引，跳过创建"
fi
# 创建染色体大小文件
cut -f1,2 ${REF_GENOME}.fai > ${JUICEBOX_DIR}/chrom.sizes 2> ${LOG_DIR}/chrom_sizes_${JOB_ID}.log
check_status "染色体大小文件生成"
##########################################################
# 3. Hi-C数据比对（使用Chromap）
##########################################################
echo "[STEP] 使用Chromap比对Hi-C reads... $(date)"
# Chromap比对参数说明：
# --preset hic: 使用Hi-C专用预设参数
# -t: 线程数
# -x: 索引文件
# -1/-2: 双端测序文件
# -o: 输出BAM文件
# --low-mem: 低内存模式（适用于大基因组）
# --remove-pcr-duplicates: 移除PCR重复
chromap \
--preset hic \
-t ${SLURM_NTASKS} \
-x ${REF_GENOME}.chromap.idx \
-1 ${READ1} \
-2 ${READ2} \
-o ${ALIGN_DIR}/aligned.bam \
--low-mem \
--remove-pcr-duplicates \
2> ${LOG_DIR}/chromap_align_${JOB_ID}.log
check_status "Chromap比对"
# 排序BAM文件
echo "[INFO] 排序比对结果..."
samtools sort -@ ${SLURM_NTASKS} -m 4G -T ${TMP_DIR}/sort_temp -o ${ALIGN_DIR}/aligned.sorted.bam ${ALIGN_DIR}/aligned.bam 2> ${LOG_DIR}/samtools_sort_${JOB_ID}.log
check_status "BAM排序"
# 索引BAM文件
samtools index ${ALIGN_DIR}/aligned.sorted.bam 2> ${LOG_DIR}/samtools_index_${JOB_ID}.log || {
echo "[WARNING] BAM索引创建失败，继续执行... $(date)"
}
##########################################################
# 4. 使用Yahs进行
Scaffolding
##########################################################
echo "[STEP] Yahs
scaffolding... $(date)"
# 运行Yahs
echo "[INFO] 运行Yahs
scaffolding..."
yahs \
-o ${SCAFFOLD_DIR}/yahs_out \
${REF_GENOME} \
${ALIGN_DIR}/aligned.sorted.bam 2> ${LOG_DIR}/yahs_run_${JOB_ID}.log
check_status "Yahs运行"
##########################################################
# 5. 转换为Juicer格式
##########################################################
echo "[STEP] 转换为Juicer格式... $(date)"
# 使用Yahs内置转换功能
echo "[METHOD] 使用Yahs内置转换..."
yahs juicer \
${SCAFFOLD_DIR}/yahs_out.bin \
${JUICEBOX_DIR}/chrom.sizes \
${SCAFFOLD_DIR}/yahs_out_scaffolds_final.agp \
${REF_GENOME} \
${JUICEBOX_DIR}/juicer 2> ${LOG_DIR}/yahs_juicer_${JOB_ID}.log
if [[ $? -ne 0 ]]; then
# 备用方法：使用samtools和awk处理
echo "[METHOD] Yahs内置转换失败，使用备用转换方法..."
# 步骤1: 提取有效交互
echo "[SUBSTEP] 提取有效交互..."
samtools view -h ${SCAFFOLD_DIR}/yahs_out.bin | \
awk 'BEGIN{OFS="\t"} {
if($1 ~ /^@/) { next } # 跳过头部
if($7 != "=") { next } # 只保留正常配对的reads
split($1, a, "/"); read_id = a[1]
if(read_id == prev_id) {
# 输出成对reads
print prev_chr, prev_pos, prev_pos + length(prev_seq), $3, $4, $4 + length($10)
read_id = "" # 避免重复输出
} else {
# 保存当前read信息
prev_id = read_id
prev_chr = $3
prev_pos = $4
prev_seq = $10
}
}' > ${JUICEBOX_DIR}/interactions.bedpe 2> ${LOG_DIR}/interactions_extract_${JOB_ID}.log
check_status "交互提取"
# 步骤2: 转换为Juicer格式
echo "[SUBSTEP] 转换为Juicer矩阵..."
awk 'BEGIN{OFS="\t"} {
# Juicer格式: <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2>
# 计算中点位置
pos1 = int(($2 + $3) / 2)
pos2 = int(($5 + $6) / 2)
# 输出交互矩阵
print 0, $1, pos1, 0, 0, $4, pos2, 1
}' ${JUICEBOX_DIR}/interactions.bedpe > ${JUICEBOX_DIR}/juicer.2.txt 2> ${LOG_DIR}/juicer_convert_${JOB_ID}.log
check_status "Juicer格式转换"
# 步骤3: 创建片段文件
echo "[SUBSTEP] 创建片段文件..."
awk 'BEGIN{OFS="\t"} {
print $1, 0, $2, 1
}' ${JUICEBOX_DIR}/chrom.sizes > ${JUICEBOX_DIR}/juicer.3.txt 2> ${LOG_DIR}/juicer_fragments_${JOB_ID}.log
check_status "片段文件创建"
# 复制染色体大小文件
cp ${JUICEBOX_DIR}/chrom.sizes ${JUICEBOX_DIR}/juicer.chromsizes
fi
##########################################################
# 6. 生成.hic文件
##########################################################
echo "[STEP] 生成.hic文件... $(date)"
# 排序Juicer文件
echo "[INFO] 排序Juicer输入文件..."
sort -S 32G -T ${TMP_DIR} --parallel=${SLURM_NTASKS} \
-k2,2d -k6,6d ${JUICEBOX_DIR}/juicer.2.txt > ${JUICEBOX_DIR}/juicer.2.sorted.txt 2> ${LOG_DIR}/juicer_sort_${JOB_ID}.log || {
echo "[WARNING] 排序失败，使用原始文件... $(date)"
cp ${JUICEBOX_DIR}/juicer.2.txt ${JUICEBOX_DIR}/juicer.2.sorted.txt
}
# 使用juicer_tools创建.hic文件
echo "[INFO] 运行juicer_tools..."
# 尝试查找juicer_tools路径
JUICER_TOOLS=$(which juicer_tools 2>/dev/null)
if [ -z "$JUICER_TOOLS" ]; then
JUICER_TOOLS="java -jar $(find ${CONDA_PREFIX}/share -name 'juicer_tools*.jar' | head -n1)"
fi
# 运行juicer_tools
$JUICER_TOOLS pre \
-j ${SLURM_NTASKS} \
-t ${TMP_DIR} \
${JUICEBOX_DIR}/juicer.2.sorted.txt \
${JUICEBOX_DIR}/aligned_${JOB_ID}.hic \
${JUICEBOX_DIR}/juicer.chromsizes 2> ${LOG_DIR}/juicer_pre_${JOB_ID}.log || {
echo "[ERROR] .hic文件生成失败! $(date)"
# 备选方法：使用Yahs的替代方案
echo "[FIX] 尝试Yahs替代方案..."
yahs ${REF_GENOME} ${ALIGN_DIR}/aligned.sorted.bam \
-o ${SCAFFOLD_DIR}/yahs_alt \
--output-hic ${JUICEBOX_DIR}/aligned_${JOB_ID}.hic \
2> ${LOG_DIR}/yahs_alt_${JOB_ID}.log || {
echo "[CRITICAL] 所有.hic生成方法均失败! $(date)"
exit 1
}
}
##########################################################
# 7. 结果验证与报告
##########################################################
echo "[STEP] 验证结果... $(date)"
# 计算运行时间
END_TIME=$(date +%s)
RUNTIME=$((END_TIME - START_TIME))
RUNTIME_STR=$(printf "%02d:%02d:%02d" $((RUNTIME/3600)) $((RUNTIME%3600/60)) $((RUNTIME%60)))
# 验证.hic文件
VALID_LOG="${LOG_DIR}/validate_${JOB_ID}.log"
$JUICER_TOOLS validate ${JUICEBOX_DIR}/aligned_${JOB_ID}.hic > ${VALID_LOG} 2>&1
VALIDATION_EXIT=$?
# 生成统计报告
REPORT_FILE="${LOG_DIR}/final_report_${JOB_ID}.txt"
echo "==== Chromap Hi-C分析结果报告 ====" > ${REPORT_FILE}
echo "任务ID: ${JOB_ID}" >> ${REPORT_FILE}
echo "开始时间: $(date -d @${START_TIME})" >> ${REPORT_FILE}
echo "结束时间: $(date -d @${END_TIME})" >> ${REPORT_FILE}
echo "运行时长: ${RUNTIME_STR}" >> ${REPORT_FILE}
echo ".hic文件: ${JUICEBOX_DIR}/aligned_${JOB_ID}.hic" >> ${REPORT_FILE}
echo "文件大小: $(du -sh ${JUICEBOX_DIR}/aligned_${JOB_ID}.hic | cut -f1)" >> ${REPORT_FILE}
echo "验证结果: $(grep -i 'valid' ${VALID_LOG} | head -1 | cut -d':' -f2-)" >> ${REPORT_FILE}
# 添加Yahs输出统计
echo -e "\n==== Yahs
Scaffolding 统计 ====" >> ${REPORT_FILE}
grep -A 5 "
Scaffolding statistics" ${LOG_DIR}/yahs_run_${JOB_ID}.log >> ${REPORT_FILE}
# 添加Chromap比对统计
echo -e "\n==== Chromap 比对统计 ====" >> ${REPORT_FILE}
grep -A 10 "Summary of mapping" ${LOG_DIR}/chromap_align_${JOB_ID}.log >> ${REPORT_FILE}
# 添加.hic文件统计
if [[ ${VALIDATION_EXIT} -eq 0 ]]; then
echo -e "\n==== Hi-C 交互统计 ====" >> ${REPORT_FILE}
$JUICER_TOOLS stats ${JUICEBOX_DIR}/aligned_${JOB_ID}.hic >> ${REPORT_FILE} 2>> ${LOG_DIR}/stats_${JOB_ID}.log
fi
##########################################################
# 8. 清理与完成
##########################################################
echo "[INFO] 清理临时文件... $(date)"
# 保留中间文件供调试
rm -f ${ALIGN_DIR}/aligned.bam
rm -f ${JUICEBOX_DIR}/interactions.bedpe
rm -f ${JUICEBOX_DIR}/juicer.2.txt
rm -f ${JUICEBOX_DIR}/juicer.2.sorted.txt
echo "[SUCCESS] Chromap Hi-C分析完成! $(date)"
echo "结果文件: ${JUICEBOX_DIR}/aligned_${JOB_ID}.hic"
echo "报告文件: ${REPORT_FILE}"
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