FATAL ERROR ML150008291L1C001R00101473806 ML150008291L1C001R00101473960 Be sure that the sam files have the same read order If using Bowtie2 or Hisat2 add the --reorder option

[ZED-rookie]

Hello,
I have a problem as follows:
===Start at 2026年 03月 17日 星期二 23:05:05 CST===
INFO:hicexplorer.lib.buildMatrixMethods:reading /home/shenzhenyang/data/shenzhenyang/09_HiC-test/04-rawfastq/aligned/muscle_1.sorted-byreadname.bam and /home/shenzhenyang/data/shenzhenyang/09_HiC-test/04-ra
wfastq/aligned/muscle_2.sorted-byreadname.bam to build hic_matrix

INFO:hicexplorer.lib.buildMatrixMethods:dangling sequences to check are {'GATC': {'pat_forw': 'GATC', 'pat_rev': 'GATC'}}

Traceback (most recent call last):
File "/home/shenzhenyang/Software/miniconda3/envs/hicexplorer/bin/hicBuildMatrix", line 7, in
main()
File "/home/shenzhenyang/Software/miniconda3/envs/hicexplorer/lib/python3.12/site-packages/hicexplorer/hicBuildMatrix.py", line 265, in main
createMatrix(pOutFileName=args.outFileName, pMaxDistance=args.maxDistance, pMaxLibraryInsertSize=args.maxLibraryInsertSize, pQCfolder=args.QCfolder,
File "/home/shenzhenyang/Software/miniconda3/envs/hicexplorer/lib/python3.12/site-packages/hicexplorer/lib/buildMatrixMethods.py", line 1068, in createMatrix
one_mate_low_quality_, iter_num_ = readBamFiles(pFileOneIterator=str1,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/shenzhenyang/Software/miniconda3/envs/hicexplorer/lib/python3.12/site-packages/hicexplorer/lib/buildMatrixMethods.py", line 494, in readBamFiles
assert mate1.qname == mate2.qname, "FATAL ERROR {} {} "
^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: FATAL ERROR ML150008291L1C001R00101473806 ML150008291L1C001R00101473960 Be sure that the sam files have the same read order If using Bowtie2 or Hisat2 add the --reorder option

This is my code to filter, map and build matrix:
fastp --qualified_quality_phred 20 --length_required 50
--compression 4 --thread 16
--json ~/data/shenzhenyang/09_HiC-test/04-rawfastq/muscle_1.json
--html ~/data/shenzhenyang/09_HiC-test/04-rawfastq/muscle_1.html
-i ~/data/shenzhenyang/09_HiC-test/04-rawfastq/muscle_1.fq.gz
-o ~/data/shenzhenyang/09_HiC-test/04-rawfastq/muscle_1.clean.fastq.gz &

fastp --qualified_quality_phred 20 --length_required 50
--compression 4 --thread 16
--json ~/data/shenzhenyang/09_HiC-test/04-rawfastq/muscle_2.json
--html ~/data/shenzhenyang/09_HiC-test/04-rawfastq/muscle_2.html
-i ~/data/shenzhenyang/09_HiC-test/04-rawfastq/muscle_2.fq.gz
-o ~/data/shenzhenyang/09_HiC-test/04-rawfastq/muscle_2.clean.fastq.gz &

bwa mem
-A1 -B4 -E50 -L0
-t 30
~/data/shenzhenyang/09_HiC-test/03-JiYingKe/ref/genome
/data/shenzhenyang/09_HiC-test/04-rawfastq/muscle_2.clean.fastq.gz
2>/data/shenzhenyang/09_HiC-test/04-rawfastq/logs/muscle_2_bwa.log
| samtools view -hb --threads 30 -o ~/data/shenzhenyang/09_HiC-test/04-rawfastq/aligned/muscle_2.bam - &
bwa mem
-A1 -B4 -E50 -L0
-t 30
~/data/shenzhenyang/09_HiC-test/03-JiYingKe/ref/genome
/data/shenzhenyang/09_HiC-test/04-rawfastq/muscle_1.clean.fastq.gz
2>/data/shenzhenyang/09_HiC-test/04-rawfastq/logs/muscle_1_bwa.log
| samtools view -hb --threads 30 -o ~/data/shenzhenyang/09_HiC-test/04-rawfastq/aligned/muscle_1.bam - &

#排序
samtools sort -n -@ 30 -o ~/data/shenzhenyang/09_HiC-test/04-rawfastq/aligned/muscle_2.sorted-byreadname.bam
~/data/shenzhenyang/09_HiC-test/04-rawfastq/aligned/muscle_1.bam &
samtools sort -n -@ 30 -o ~/data/shenzhenyang/09_HiC-test/04-rawfastq/aligned/muscle_1.sorted-byreadname.bam
~/data/shenzhenyang/09_HiC-test/04-rawfastq/aligned/muscle_2.bam &

echo "===Start at $(date)===" >> ~/data/shenzhenyang/09_HiC-test/04-rawfastq/logs/muscle_hicBuildMatrix-byreadname.log
hicBuildMatrix
--samFiles ~/data/shenzhenyang/09_HiC-test/04-rawfastq/aligned/muscle_1.sorted-byreadname.bam
~/data/shenzhenyang/09_HiC-test/04-rawfastq/aligned/muscle_2.sorted-byreadname.bam
--genomeAssembly ~/data/shenzhenyang/09_HiC-test/04-rawfastq/ref/genome.fa
--outBam ~/data/shenzhenyang/09_HiC-test/04-rawfastq/hic_matrix/Raw/muscle.bam
--outFileName ~/data/shenzhenyang/09_HiC-test/04-rawfastq/hic_matrix/Raw/muscle.cool
--QCfolder ~/data/shenzhenyang/09_HiC-test/04-rawfastq/hic_matrix/Raw/muscle
--restrictionCutFile ~/data/shenzhenyang/09_HiC-test/03-JiYingKe/ref/chr1-18_rest_site.bed
--binSize 1000
--threads 100
--minDistance 500
--maxLibraryInsertSize 1500
--inputBufferSize 400000
--restrictionSequence GATC
--danglingSequence GATC \

~/data/shenzhenyang/09_HiC-test/04-rawfastq/logs/muscle_hicBuildMatrix-byreadname.log 2>&1
echo "===End at $(date)===" >> ~/data/shenzhenyang/09_HiC-test/04-rawfastq/logs/muscle_hicBuildMatrix-byreadname.log

[ZED-rookie]

I saw that others had the same problem as me. #562 #703
Version bwa : 0.7.17-r1188, hicexplorer 3.7.6