HiC-Pro_3.1.0 failed to trim 3' end of the unmapped reads?

[ddzhang3]

We are constructing Hi-C library using MboI enzyme. When I run the HiC-Pro (version 3.1.0) pipeline, the mapping step2 seems to fail in trim 3' end of the unmapped reads, as following:

##Fastq file: bowtie_results/bwt2_global/k562-con-7c/k562-con-7c_L2_M001.R1_hg38.bwt2glob.unmap.fastq
##Restriction sites (n=1):
^GATC
##Output File: bowtie_results/bwt2_local/k562-con-7c/k562-con-7c_L2_M001.R1_hg38.bwt2glob.unmap_trimmed.fastq
##Trimmed reads: 0

However, when I use HiCUP, which trim 3' end at the very first step, the trimmed reads rate is 46.23% for the same fastq. As a result, I am confused about this. Can you give some advice?

[nservant]

did you check the LIGATION SITE (not restriction site) you provided to HiC-Pro ?