HiC-Protojuice box error, hic format file cannot do loop calling

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yue zhu

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Jan 8, 2022, 11:11:44 PM1/8/22

to HiC-Pro

Dear all!

I met a problem when I tried to convert the HiC output to juicebox input to call loops on my data (about 1 billion validpairs).

The following is the command line I used:

hicpro2juicebox.sh /home/yhdong/zhuyue/20210510_ZYY_NPC_HiC/data/kosample/npc_1038000000_merge_ko.allValidPairs -g mm10 -j /home/yhdong/software/juicer_tools_2.13.0.jar -r /home/yhdong/software/HiC-Pro_2.11.4/annotation/MboI_mm10.bed -o ./

then，I GOT A HIC FILE "npc_1038000000_merge_ko.validPairs.hic" ,IT can be visualized on juicerbox, but IT cannot call loop, compartment.

WHEN I USE JUICER HICCUP to call loops,:

"java -jar ~/software/juicer_tools_1.22.01.jar hiccups --threads 28 -r 20000 ../npc_1038000000_merge_ko.validPairs.hic ./"

It didn't work.

I got some error info like this:

Resolution 20000 not available.

Data not available for chr1 at 5000 resolution

Data not available for chr2 at 5000 resolution

Data not available for chr3 at 5000 resolution

Data not available for chr4 at 5000 resolution

Data not available for chr5 at 5000 resolution

Data not available for chr6 at 5000 resolution

Data not available for chr7 at 5000 resolution

Data not available for chr8 at 5000 resolution

Data not available for chr9 at 5000 resolution

Data not available for chr10 at 5000 resolution

Data not available for chr11 at 5000 resolution

Data not available for chr12 at 5000 resolution

Data not available for chr13 at 5000 resolution

Data not available for chr14 at 5000 resolution

Data not available for chr15 at 5000 resolution

Data not available for chr16 at 5000 resolution

Data not available for chr17 at 5000 resolution

Data not available for chr18 at 5000 resolution

Data not available for chr19 at 5000 resolution

Data not available for chrM at 5000 resolution

Data not available for chrX at 5000 resolution

Data not available for chrY at 5000 resolution

Data not available for chr1 at 10000 resolution

Data not available for chr2 at 10000 resolution

Data not available for chr3 at 10000 resolution

Data not available for chr4 at 10000 resolution

Data not available for chr5 at 10000 resolution

Data not available for chr6 at 10000 resolution

Data not available for chr7 at 10000 resolution

Data not available for chr8 at 10000 resolution

Data not available for chr9 at 10000 resolution

Data not available for chr10 at 10000 resolution

Data not available for chr11 at 10000 resolution

Data not available for chr12 at 10000 resolution

Data not available for chr13 at 10000 resolution

Data not available for chr14 at 10000 resolution

Data not available for chr15 at 10000 resolution

Data not available for chr16 at 10000 resolution

Data not available for chr17 at 10000 resolution

Data not available for chr18 at 10000 resolution

Data not available for chr19 at 10000 resolution

Data not available for chrM at 10000 resolution

Data not available for chrX at 10000 resolution

Data not available for chrY at 10000 resolution

Data not available for chr1 at 25000 resolution

Data not available for chr2 at 25000 resolution

Data not available for chr3 at 25000 resolution

Data not available for chr4 at 25000 resolution

Data not available for chr5 at 25000 resolution

Data not available for chr6 at 25000 resolution

Data not available for chr7 at 25000 resolution

Data not available for chr8 at 25000 resolution

Data not available for chr9 at 25000 resolution

Data not available for chr10 at 25000 resolution

Data not available for chr11 at 25000 resolution

Data not available for chr12 at 25000 resolution

Data not available for chr13 at 25000 resolution

Data not available for chr14 at 25000 resolution

Data not available for chr15 at 25000 resolution

Data not available for chr16 at 25000 resolution

Data not available for chr17 at 25000 resolution

Data not available for chr18 at 25000 resolution

Data not available for chr19 at 25000 resolution

Data not available for chrM at 25000 resolution

Data not available for chrX at 25000 resolution

Data not available for chrY at 25000 resolution

It seems that the data not available at 25000 resolution, but when I change another data which is smaller(about 300million validpairs), it works.

I AM confused whether it is my data size problem or my data lost something when changing the format