Problem converting allValidPairs files to .hic using hicpro2juicebox.sh

[GianMa]

Good evening,
I am trying to perform the conversion as in the title but I am blocked by this error:

Problem with creating fragment-delimited maps, NullPointerException.
This could be due to a null fragment map or to a mismatch in the chromosome name in the fragment map vis-a-vis the input file or chrom.sizes file.


The command I am running is the following:

ls *.txt | parallel -j 3 "hicpro2juicebox.sh -i {} -j ~/juicer_tools/juicer_tools.jar -g ~/utilities/chr_hg19.size -r ~/utilities/mboi_restriction_fragments_hg19.bed -o ../pro2hic/"

(juicer tools have been installed from the latest github, 2.x - hicpro2juicebox has been installed from the current github repo)

Concerning the problem, I have found this thread ( https://groups.google.com/g/hic-pro/c/ylonMED_EfE/m/yotT1BZNAwAJ ), but I have already checked that chr names match between chr size file, the validPairs, and the fragments.

I don't know how to further proceed as I don't understand what else could be wrong in my input.


Here are the heads of my files:

Valid pairs
K00146:HLNFGBBXX171004:HLNFGBBXX:4:2118:3427:4163       chr1    13041   -       chr16   68206970        -       322     HIC_chr1_6      HIC_chr16_155342        32      23
K00146:HLNFGBBXX171004:HLNFGBBXX:4:1107:18751:25755     chr1    13049   -       chr19   38355525        +       384     HIC_chr1_6      HIC_chr19_105650        32      23
K00146:HLNFGBBXX171004:HLNFGBBXX:4:2227:11931:48790     chr1    13050   -       chr16   90136329        +       381     HIC_chr1_6      HIC_chr16_214433        32      42
K00146:HLNFGBBXX171004:HLNFGBBXX:4:1212:27661:25087     chr1    13050   -       chr17   80799638        +       417     HIC_chr1_6      HIC_chr17_218428        32      42
K00146:HLNFGBBXX171004:HLNFGBBXX:4:1113:15585:7082      chr1    13051   -       chr6    376369  +       383     HIC_chr1_6      HIC_chr6_739    32      42
K00146:HLNFGBBXX171004:HLNFGBBXX:4:1108:17858:22063     chr1    13051   -       chr6    25653884        +       332     HIC_chr1_6      HIC_chr6_64932  32      42
K00146:HLNFGBBXX171004:HLNFGBBXX:4:2101:18730:41475     chr1    13051   +       chr17   3758676 -       408     HIC_chr1_6      HIC_chr17_11443 32      42

chr sizes
chr1    249250621
chr2    243199373
chr3    198022430
chr4    191154276
chr5    180915260
chr6    171115067
chr7    159138663
chr8    146364022
chr9    141213431
chr10   135534747

restriction sites
chr1    0       11159   HIC_chr1_1      0       +
chr1    11159   12410   HIC_chr1_2      0       +
chr1    12410   12460   HIC_chr1_3      0       +
chr1    12460   12685   HIC_chr1_4      0       +
chr1    12685   12828   HIC_chr1_5      0       +
chr1    12828   13314   HIC_chr1_6      0       +
chr1    13314   13419   HIC_chr1_7      0       +
chr1    13419   13565   HIC_chr1_8      0       +
chr1    13565   13697   HIC_chr1_9      0       +
chr1    13697   13914   HIC_chr1_10     0       +

[GianMa]

Edit:
I noticed that the restriction fragment file I obtained was missing chrX and chrY.
I am now trying to exclude them from all files to see if this would work.
I will update you on the result, apologize for the mistake.