Allelic analysis HiC-Pro G2 genome not mapping

[luckysardar]

Dear I am trying to do allelic analysis Hic data getting same error G2 is mapping reads are zero and iced normalisation step getting error. I used bellow command to run analysis. non allelic analysis running completely good . I tried many publically available data with different strain cross like 129S vs CAST and B6 vs PWK got same error I am unable to find solution where its going wrong please help me

bowtie2 allespe.stat file looks like below HiC-Pro_3.1.0/scripts/markAllelicStatus.py bam=bowtie_results/bwt2/Sample1/subset_masked_mm10.bwt2pairs.bam snpFile=mm10_snps_C57b6_PWK_PhJ.vcf tag=XA output=bowtie_results/bwt2/Sample1/subset_masked_mm10.bwt2pairs_allspe.bam verbose=True

Total number of snps loaded 17046154.0

Total number of reads 353850 100 Number of reads with at least one 'N' 368870 104.245 Number of reads assigned to ref genome 91967 25.99 Number of reads assigned to alt genome 0 0.0 Number of conflicting reads 0 0.0 Number of unassigned reads 261883 74.01

code used generate VCF and masked genome

`extract_snps.py -i mgp.v5.merged.snps_all.dbSNP142.vcf -a PWK_PhJ> mm10_snps_C57b6_PWK_PhJ.vcf

bedtools maskfasta -fi mm10.fa -bed mm10_snps_C57b6_PWK_PhJ.vcf -fo masked_mm10.fa

bowtie2-build masked_mm10.fa masked_mm10 --threads 6

HiC-Pro -c config_test_as.txt -i 01_Fastq/ -o 03_output2`

please suggest me where I am going wrong

Thank you