haphic pipeline

[tky199996]

Hi, I used haphic pipeline and everything worked fine, but recently when I used purge_dups to remove redundancy from my assembly sequence and then used haphic pipeline, the following error message appeared. I don't know why, can you help me take a look? It is worth noting that when I used YaHS to mount my sequence after removing redundancy, it did not report an error message.

[zengxiaofei]

The FASTA file you input does not match the BAM file.

[tky199996]

您输入的FASTA文件与BAM文件不匹配。
Thank you for your prompt reply. My fasta file is the fasta sequence after I used hifiasm to assemble and purgeddups to remove redundancy, and my bam file is HiC data. It should match. Is it because my fasta sequence uses purgeddups to remove redundancy? I found that when I run the haphic pipeline, the fasta sequence does not build an index. I will contact you after I try it. Thank you again.

[zengxiaofei]

My fasta file is the fasta sequence after I used hifiasm to assemble and purgeddups to remove redundancy, and my bam file is HiC data.

Did you realign the Hi-C reads to the assembly after purging duplicates? If not, these two files do not match. This means that some reference IDs present in the BAM file do not exist in the FASTA file, which would cause HapHiC to throw an error. I've deliberately made the ID checking more stringent to prevent users from using incorrect or mismatched files.

[tky199996]

My fasta file is the fasta sequence after I used hifiasm to assemble and purgeddups to remove redundancy, and my bam file is HiC data.

Did you realign the Hi-C reads to the assembly after purging duplicates? If not, these two files do not match.

Oh! Yes! Looks like I made a stupid mistake. Thanks for your help, I will try to run it again!