unknown "Terminated" when Running step "Combine R1/R2 alignment files"

[MaybeBio]

I finished the previous 2 steps successfully ：
Bowtie2 alignment step1
Bowtie2 alignment step2

but the 3rd step——Combine R1/R2 alignment files，
it shows an error

here is my whole log：
`nohup: ignoring input

Run HiC-Pro 3.1.0

Sat Feb 22 05:49:38 PM CST 2025
Bowtie2 alignment step1 ...
Logs: logs/N_1/mapping_step1.log
Logs: logs/N_2/mapping_step1.log
Logs: logs/T_1/mapping_step1.log
Logs: logs/T_2/mapping_step1.log
Logs: logs/TN_1/mapping_step1.log
Logs: logs/TN_2/mapping_step1.log

---

Tue Feb 25 10:10:22 PM CST 2025
Bowtie2 alignment step2 ...
Logs: logs/N_1/mapping_step2.log
Logs: logs/N_2/mapping_step2.log
Logs: logs/T_1/mapping_step2.log
Logs: logs/T_2/mapping_step2.log
Logs: logs/TN_1/mapping_step2.log
Logs: logs/TN_2/mapping_step2.log

---

Wed Feb 26 10:35:28 PM CST 2025
Combine R1/R2 alignment files ...
Logs: logs/N_1/mapping_combine.log
make: *** [/home/nicai_zht/HiC-Pro_3.1.0/bin/../scripts//Makefile:115: bowtie_combine] Terminated
`

and the specific one——logs/N_1/mapping_combine.log，presented below：

/home/nicai_zht/miniconda3/envs/hic-pro/bin/samtools merge -@ 30 -n -f bowtie_results/bwt2/N_1/N-1_R2_Homo_sapiens_GRCh38_1Y.bwt2merged.bam bowtie_results/bwt2_global/N_1/N-1_R2_Homo_sapiens_GRCh38_1Y.bwt2glob.bam bowtie_results/bwt2_local/N_1/N-1_R2_Homo_sapiens_GRCh38_1Y.bwt2glob.unmap_bwt2loc.bam /home/nicai_zht/miniconda3/envs/hic-pro/bin/samtools merge -@ 30 -n -f bowtie_results/bwt2/N_1/N-1_R1_Homo_sapiens_GRCh38_1Y.bwt2merged.bam bowtie_results/bwt2_global/N_1/N-1_R1_Homo_sapiens_GRCh38_1Y.bwt2glob.bam bowtie_results/bwt2_local/N_1/N-1_R1_Homo_sapiens_GRCh38_1Y.bwt2glob.unmap_bwt2loc.bam /home/nicai_zht/miniconda3/envs/hic-pro/bin/samtools sort -@ 30 -m 3333M -n -T tmp/N-1_R2_Homo_sapiens_GRCh38_1Y -o bowtie_results/bwt2/N_1/N-1_R2_Homo_sapiens_GRCh38_1Y.bwt2merged.sorted.bam bowtie_results/bwt2/N_1/N-1_R2_Homo_sapiens_GRCh38_1Y.bwt2merged.bam /home/nicai_zht/miniconda3/envs/hic-pro/bin/samtools sort -@ 30 -m 3333M -n -T tmp/N-1_R1_Homo_sapiens_GRCh38_1Y -o bowtie_results/bwt2/N_1/N-1_R1_Homo_sapiens_GRCh38_1Y.bwt2merged.sorted.bam bowtie_results/bwt2/N_1/N-1_R1_Homo_sapiens_GRCh38_1Y.bwt2merged.bam

i see no problem here, it just Terminated ...

my config file presented blow:
`# Please change the variable settings below if necessary

#########################################################################

Paths and Settings - Do not edit !

#########################################################################

TMP_DIR = tmp
LOGS_DIR = logs
BOWTIE2_OUTPUT_DIR = bowtie_results
MAPC_OUTPUT = hic_results
RAW_DIR = rawdata

#######################################################################

SYSTEM AND SCHEDULER - Start Editing Here !!

#######################################################################
N_CPU = 30
SORT_RAM = 100000M
LOGFILE = hicpro.log

JOB_NAME = zht_hic
JOB_MEM = 120gb
JOB_WALLTIME =
JOB_QUEUE =
JOB_MAIL =

#########################################################################

Data

#########################################################################

PAIR1_EXT = _R1
PAIR2_EXT = _R2

#######################################################################

Alignment options

#######################################################################

MIN_MAPQ = 10

BOWTIE2_IDX_PATH = /data1/project/hic_lung/whfs-xs-242342_202502170910/whfs-xs-242342_hic_rawdata_20241202/GRCh38-GENCODEv44_build
BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder
BOWTIE2_LOCAL_OPTIONS = --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder

#######################################################################

Annotation files

#######################################################################

REFERENCE_GENOME = Homo_sapiens_GRCh38_1Y
GENOME_SIZE = /data1/project/hic_lung/whfs-xs-242342_202502170910/whfs-xs-242342_hic_rawdata_20241202/GRCh38-GENCODEv44_build/Homo_sapiens.GRCh38_1Y.chrom.sizes

#######################################################################

Allele specific analysis

#######################################################################

ALLELE_SPECIFIC_SNP =

#######################################################################

Capture Hi-C analysis

#######################################################################

CAPTURE_TARGET =
REPORT_CAPTURE_REPORTER = 1

#######################################################################

Digestion Hi-C

#######################################################################

GENOME_FRAGMENT = /data1/project/hic_lung/whfs-xs-242342_202502170910/whfs-xs-242342_hic_rawdata_20241202/GRCh38-GENCODEv44_build/Homo_sapiens_GRCh38_1Y_mboi.bed
LIGATION_SITE = GATCGATC
MIN_FRAG_SIZE =
MAX_FRAG_SIZE =
MIN_INSERT_SIZE =
MAX_INSERT_SIZE =

#######################################################################

Hi-C processing

#######################################################################

MIN_CIS_DIST =
GET_ALL_INTERACTION_CLASSES = 1
GET_PROCESS_SAM = 0
RM_SINGLETON = 1
RM_MULTI = 1
RM_DUP = 1

#######################################################################

Contact Maps

#######################################################################

BIN_SIZE = 10000 20000 40000 100000
MATRIX_FORMAT = upper

#######################################################################

Normalization

#######################################################################
MAX_ITER = 100
FILTER_LOW_COUNT_PERC = 0.02
FILTER_HIGH_COUNT_PERC = 0
EPS = 0.1
`

Any ideas..?

THX