On the issue of duplicated chromosomes
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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？
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and my pairs file like this
pairs format v1.0.0
#chromsize: chr1 195471971
#chromsize: chr2 182113224
#chromsize: chrX 171031299
#chromsize: chr3 160039680
#chromsize: chr4 156508116
#chromsize: chr5 151834684
#chromsize: chr6 149736546
#chromsize: chr7 145441459
#chromsize: chr10 130694993
#chromsize: chr8 129401213
#chromsize: chr14 124902244
#chromsize: chr9 124595110
#chromsize: chr11 122082543
#chromsize: chr13 120421639
#chromsize: chr12 120129022
#chromsize: chr15 104043685
#chromsize: chr16 98207768
#chromsize: chr17 94987271
#chromsize: chrY 91744698
#chromsize: chr18 90702639
#chromsize: chr19 61431566
#chromsize: chrM 16299
#samheader: @sq SN:chr1 LN:195471971
#samheader: @sq SN:chr10 LN:130694993
#samheader: @sq SN:chr11 LN:122082543
#samheader: @sq SN:chr12 LN:120129022
#samheader: @sq SN:chr13 LN:120421639
#samheader: @sq SN:chr14 LN:124902244
#samheader: @sq SN:chr15 LN:104043685
#samheader: @sq SN:chr16 LN:98207768
#samheader: @sq SN:chr17 LN:94987271
#samheader: @sq SN:chr18 LN:90702639
#samheader: @sq SN:chr19 LN:61431566
#samheader: @sq SN:chr2 LN:182113224
#samheader: @sq SN:chr3 LN:160039680
#samheader: @sq SN:chr4 LN:156508116
#samheader: @sq SN:chr5 LN:151834684
#samheader: @sq SN:chr6 LN:149736546
#samheader: @sq SN:chr7 LN:145441459
#samheader: @sq SN:chr8 LN:129401213
#samheader: @sq SN:chr9 LN:124595110
#samheader: @sq SN:chrM LN:16299
#samheader: @sq SN:chrX LN:171031299
#samheader: @sq SN:chrY LN:91744698
#samheader: @pg ID:bwa PN:bwa VN:0.7.17-r1188 CL:bwa mem /cluster/home/Kangwen/common/mm10/mm10.fa -t 60 trimmed-pair1.fastq.gz trimmed-pair2.fastq.gz
#samheader: @pg ID:samtools PN:samtools PP:bwa VN:1.17 CL:samtools view -@ 60-S -b -o SRR22522721.bam SRR22522721.sam