error when running arrowhead with .hic file converted from hicpro output

[Moon Traveler]

Hello,

After convert allValidPairs from hicpro output to .hic format, I tried to run arrowhead, however got the following error:
Could not read hic file: No enum constant juicebox.windowui.

NormalizationType.SCALE

Could anyone help me with this? Thanks in advance!

[Ray Oquendo]

Hi Moon Traveler,

We are relatively new to HiCPro, just started in 2018.  We have a number of HiCPro runs and multiple output files.

We need to take the HiCPro output files (allValidPairs) and convert it to .hic file format.  But have not been able to get the right tools.

Can you tell me which tools you used?  And can you share the script used to perform the conversion?

Thanks in advance.

RayOq

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[Moon Traveler]

Hello RayOq,

I use hicpro2juicebox.sh to convert HiCPro output files(allValidPairs) to .hic format, which is part of HicPro utilities. My script is below:

hicpro2juicebox.sh -i /data/xieb2/PF_HiC/rawdata1/hic_results/data/ERR466161/ERR466161.allValidPairs -g /data/xieb2/PF_HiC/chrom_mm9.sizes -j /data/xieb2/PF_HiC_hicformat/juicer_tools_1.14.08.jar -o /data/xieb2/PF_HiC_hicformat/

-i is the directory for input file, -g is the genome size file, -j is the directory for juicebox command line tools, -o is directory for output file

For detailed info, please see the link below:

https://nservant.github.io/HiC-Pro/UTILS.html#hicpro2juicebox-sh

Hope it helps.

Best regards,

Moon Traveler

On Friday, January 17, 2020 at 1:17:10 PM UTC-5, Ray Oquendo wrote:

Hi Moon Traveler,

We are relatively new to HiCPro, just started in 2018.  We have a number of HiCPro runs and multiple output files.

We need to take the HiCPro output files (allValidPairs) and convert it to .hic file format.  But have not been able to get the right tools.

Can you tell me which tools you used?  And can you share the script used to perform the conversion?

Thanks in advance.

RayOq

On Fri, Jan 17, 2020 at 12:01 PM Moon Traveler <moonvoy...@gmail.com> wrote:

Hello,

After convert allValidPairs from hicpro output to .hic format, I tried to run arrowhead, however got the following error:
Could not read hic file: No enum constant juicebox.windowui.

NormalizationType.SCALE

Could anyone help me with this? Thanks in advance!

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[GianMa]

Hi Moon Traveler,
I am getting the exact same issue, were you able to solve this problem in the end?
Any input is appreciated.
Thank you

[Muhammad Shamim]

What version of juicer_tools was used for building the file and what version are you using for arrowhead? (there's likely a clash at that level)

You could try using the latest juicer tools jar under the github release.

[GianMa]

Good morning,
Sorry for the confusion, my issue is slightly different and it doesn't involve arrowhead, even though I get the same error.

I am trying the following:
from .allValidPairs file from hic-pro pipeline I generated .hic files using this script ( https://github.com/nservant/HiC-Pro/blob/master/bin/utils/hicpro2juicebox.sh ) and using the juice_tools ( juicer_tools_1.22.01.jar ).
This script generates the hic files, and I can load them to juicebox. However, I cannot dump them as I get the error reported above: (Could not read hic file: No enum constant juicebox.windowui. NormalizationType.SCALE)
Do you have any idea of what could be wrong?
Best

[Muhammad Shamim]

Try using a newer jar to run Arrowhead (under the Github Releases).

[GianMa]

Sorry if I am not explaining myself clearly.

I am NOT using arrowhead.
I am however getting the same error reported above after converting .allValidPairs files into .hic files and then trying to dump normalized contacts with either juice ox application or through CLI.
To me, it seems like the scripts generate the .hic files correctly, but doesn't add a variable that is required for normalization.
Please let me know if I should start a new thread instead,
Best

[Muhammad Shamim]

Ah my bad. A new thread would probably be better in that case. 

If you're not doing genome assembly, I would suggest using the latest juicer_tools.jar for building the file (i.e. update whatever the pairs script is to use the latest 2.x jar for building). Then use github.com/aidenlab/straw to stream the hic data to the language of choice.