hicpro to juice box error,hic file cannot do loop calling

[yue zhu]

Dear all!

I met a problem when I  successfully converted the HiC-Pro output (about 1 billion validpairs) to Juicebox (15g hic file) but failed to input hic file to call loops on my data .

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 to 7GB hic file and use HICCUP to call loop), it works. 

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

Can anybody help me?? Thanks in advance.

[Muhammad Shamim]

Have you loaded the file in Juicebox?

What jar version was used in the conversion script?

[yue zhu]

Hi!

 I used  juicer_tools_2.13.0.jar  in the conversion script.

and I loaded the hic file in Juicebox. It can be visualized like the screenshot below. But it cannot use BALANCED option. And I cannot use HICCUPS to call loop.

[Muhammad Shamim]

What does the map look like at higher resolutions, e.g. 5kb and 10kb? If BALANCED normalization is not working, do VC or VC_SQRT look reasonable? Or are none of them loading? (maybe be a version clash issue)

[yue zhu]

the 5kb resolution  looks like this:

and 10kb：

when I chose the normalization ，none of them loading.

maybe it's the version clash issue?

and I will try the 2.13.07 juicer_tools.jar and  juicebox.jar to transfer my hicpro format to juicebox.

Thank you!

[Pavla Navratilova]

Hi, 

I have exactly the same problem with my .hic file - it looks normal in Juicebox at the given resolution, but the normalizations are not available and the hiccups responds with the error message:

```

java -Xmx8g -jar /home/pavlan/tools/juicer/CPU/common/juicer_tools.jar hiccups --cpu --threads 20 -r 10000 inter_30.hic loops_10k
Reading file: inter_30.hic
Using the following configurations for HiCCUPS:
Config res: 10000 peak: 2 window: 5 fdr: 10% radius: 20000
WARNING - You are using the CPU version of HiCCUPS.
The GPU version of HiCCUPS is the official version and has been tested extensively.
The CPU version only searches for loops within 8MB (by default) of the diagonal and is still experimental.
Unable to assess map sparsity; continuing with HiCCUPS
Running HiCCUPS for resolution 10000
Data not available for 1H at 10000 resolution
Data not available for 2H at 10000 resolution
Data not available for 3H at 10000 resolution
Data not available for 4H at 10000 resolution
Data not available for 5H at 10000 resolution
Data not available for 6H at 10000 resolution
Data not available for 7H at 10000 resolution
Data not available for 1H at 10000 resolution
Data not available for 2H at 10000 resolution
Data not available for 3H at 10000 resolution
Data not available for 4H at 10000 resolution
Data not available for 5H at 10000 resolution
Data not available for 6H at 10000 resolution
Data not available for 7H at 10000 resolution
```

My .hic file was generated with the  Juicer 1.6

``

juicer/CPU/juicer.sh -g hv03 -D Juicer_dir -s Arima -z Juicer_dir/references/MorexV3_NOchrUn.fa -y Juicer_dir/restriction_sites/hv03_Arima.txt -p Juicer_dir/chrom_sizes/hv03.chr.sizes -f -t 40

``

[Alexander Predeus]

I have the same problem I'm pretty sure. I've used the same version of Juicer tools (1.22.01) to both generate the hic files and to run HiCCUPS. 

Is there some sort of command that can list which resolutions are contained in the hic file obtained? 

All the best, 

-- Alex

[Alexander Predeus]

To update, I've re-run the "pre" command with the newest Juicer tools (2.20.00), and then ran hiccups on these files. It worked - the error about "Data not available for chr1" etc disappeared. 

However, when I ran hiccupsdiff on the same files, it came right back? the log of the "pre" command explicitly showed writing data at the required resolutions (5k, 10k, 25k). So I'm at a loss really. 

Any help would be appreciated. 

-- Alex

[Erik Parker]

If anyone is still running into issues with this, I fixed my problems and got all of the Juicer tools steps to run by using an older version of juicer tools (version 1.19.02 specifically, downloaded from here: https://github.com/aidenlab/juicer/wiki/Download#version-11902).
Switching to this version of juicer tools also fixed issues I was running into when converting my output from HiC-Pro using the hicpro2juicebox.sh script.

Happy to share my syntax with anyone who needs it.