Why is there only one cluster in the HapHiC_cluster.log

[zhangmeng123456abc]

Hello Xiaofei,
Thank you for developing the Haphic software. my HapHiC_cluster.log have a question "<HapHiC_cluster.py> [run_mcl_clustering] The maximum number of clusters (1) is even less than the expected number of chromosomes (16). You could try higher inflation. " In this case, how to choose the "best" inflation recommendation

Thank you

[zengxiaofei]

Hi @zhangmeng123456abc,
I need more information to understand the problem:
(1) Your commands and parameters used in running HapHiC.
(2) Please upload the whole log file generated in 01.cluster
(3) Please calculate the N10-N90 and L10-L90 of the contigs input into HapHiC using this tool:

$ gunzip fa_detail.gz
$ chmod 755 fa_detail
$ fa_detail asm.fa

Best,
Xiaofei

[zhangmeng123456abc]

Hi Xiaofei,
(1)My commands and parameters used in running HapHiC: 0.bwa index asm.fa

1. bwa mem -5SP -t 28 genome.final.fasta hic.R1.fastq.gz hic.R2.fastq.gz | samblaster | samtools view - -@ 14 -S -h -b -F 256 -o HiC.bam 2. HapHic/HapHiC-main/utils/filter_bam HiC.bam 1 --nm 3 --threads 14 | samtools view - -b -@ 14 -o HiC.filtered.bam 3. HapHic/HapHiC-main/haphic cluster genome.final.fasta HiC.filtered.bam 16
   (2) The log has been uploaded
   HapHiC_cluster.log
   (3) I can't run fa detail , I use assembly-stats for N50 statistics
   sum = 442473677, n = 160, ave = 2765460.48, largest = 18480413
   N50 = 9527079, n = 16
   N60 = 7213451, n = 22
   N70 = 5827328, n = 28
   N80 = 4039110, n = 37
   N90 = 2302510, n = 51
   N100 = 29644, n = 160
   N_count = 0
   Gaps = 0

[zengxiaofei]

First, the FLAG filtering criterion you used is -F 256. This is incorrect. Supplementary alignments should be removed to make the BAM file suitable for HapHiC (HapHiC needs only two adjacent lines for each pair of reads). Please use the criteria -F 3340 that we recommended in README.md.
After making this modification, if you still encounter this error message, please try a higher inflation upper limit using the --max_inflation parameter (e.g., --max_inflation 10). A lower --bin_size may also be helpful (e.g., --bin_size 200).