On the issue of duplicated chromosomes

[HanwenZhu98]

hickit -i mus.restrict.pairs.gz -u -o - | bgzip > impute.pairs.gz [W::parse_pair_cols] unrecognized column "pair_type" will be ignored [W::parse_pair_cols] unrecognized column "mapq1" will be ignored [W::parse_pair_cols] unrecognized column "mapq2" will be ignored [W::parse_pair_cols] unrecognized column "rfrag1" will be ignored [W::parse_pair_cols] unrecognized column "rfrag_start1" will be ignored [W::parse_pair_cols] unrecognized column "rfrag_end1" will be ignored [W::parse_pair_cols] unrecognized column "rfrag2" will be ignored [W::parse_pair_cols] unrecognized column "rfrag_start2" will be ignored [W::parse_pair_cols] unrecognized column "rfrag_end2" will be ignored [M::hk_map_read] read 7168095 pairs [E::hk_sd_ploidy_XY] multiple chr contain 'X' or 'Y' in names

I always have this issue with pairs files obtained using mm10, but using hg38 or 19 will not result in such errors？ Can we add wechat for further conversation，my wechat：Nizenmebujiedianhua