Error running hiccupsdiff

[rahulk87]

Hi, I successfully ran Juicer and got the .hic and merged_loops.bedpe for both control and experimental samples. Now I am trying to run hiccupsdiff but getting below error:

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 and so on....

I am not able to understand what is wrong with the input files, can you please help, thank you in advance.

[erikpark]

I have this same issue as well. Was able to run HiCCUPS, and Arrowhead on my .hic files just fine - but HiCCUPSDiff fails. Did you have any luck figuring this out? Looks like a few people have been having this issue recently (https://groups.google.com/g/3d-genomics/c/KhTpJJSNiyg/m/HubOa8dSAwAJ, https://groups.google.com/g/3d-genomics/c/eJywI41jwV0/m/-EeIW7w9BgAJ)

[erikpark]

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.

[rahulk87]

Thanks Erik, so you did all the steps with this version or just HiCCUPSDiff?

I ran HiCCUPSDiff with this version on .hic file created with another version and it failed.

Can you please share your scripts, thanks a lot!

[erikpark]

I did all the steps with the older version of juicer tools, in my case starting all the way from hicpro2juicbox.sh - as the data I was working with were originally processed in HiCPro.

I'm posting the scripts here, I think they are well-annotated, and hopefully they are helpful for you!

Juicer scripts 2023-06-08.txt

[rahulk87]

Thanks Erik for the script, you're lucky that it worked for me.

For me v1.19.02 is unable to read my .hic files created by v.2.20.00

May be I need to run the whole pipeline with v1.19.02, but I doubt that too.

It is surprising that it didn't show any error on .hic file of HiCPro.

[erikpark]

I can confirm that I also had to run through the whole pipeline using 1.19.02. I also found that trying to use any juicer tools commands on the hic files I made with 2.20.00 didn’t work. So I redid everything with 1.19.02 and it worked fine.

[rahulk87]

I successfully generated .hic file using 1.19.02 and then ran Arrowhead and hiccups on the same .hic file but didn't get loops/contacts and getting below error.

Data not available for 1 at 5000 resolution Data not available for 10 at 5000 resolution Data not available for 11 at 5000 resolution Data not available for 11_KI270721V1_RANDOM at 5000 resolution Data not available for 12 at 5000 resolution Data not available for 13 at 5000 resolution Data not available for 14 at 5000 resolution ........................

I got this error earlier also but it was resolved when I used v2.20.00 but couldn't run hiccupsdiff successfully this version, so I was looking for solutions.

[erikpark]

Hmm, sorry it's not working for you! The only other thing I can think of is that when you are running the hicpro2Juicebox.sh script you might need to specify the genome size, and restriction fragment files (using the -g and -r flags) that you used when you originally ran HiC-Pro.

Something like this: hicpro2juicebox.sh -i CTRL_allValidPairs -g mm10_sorted_genome.fa.fai -t tmp-CTRL -o /hic2juicer -j juicer_tools_1.19.02.jar -r mm10_sorted_genome.fa.mm10_GATC_GANTC_no_chr_with_MT.bed

---

Erik Parker, PhD Biostatistician I Biostatistics Consulting Center Department of Epidemiology and Biostatistics School of Public Health-Bloomington Indiana University 2719 E. 10th Street, 224 Bloomington, IN 47408 @.**@.> biostats.indiana.eduhttps://biostats.indiana.edu/

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From: Rahul Kumar @.> Sent: Wednesday, June 14, 2023 2:35 PM To: aidenlab/juicer @.> Cc: Parker, Erik @.>; Comment @.> Subject: [External] Re: [aidenlab/juicer] Error running hiccupsdiff (Issue #312)

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I successfully generated .hic file using 1.19.02 and then ran Arrowhead and hiccups on the same .hic file but didn't get loops/contacts and getting below error.

Data not available for 1 at 5000 resolution Data not available for 10 at 5000 resolution Data not available for 11 at 5000 resolution Data not available for 11_KI270721V1_RANDOM at 5000 resolution Data not available for 12 at 5000 resolution Data not available for 13 at 5000 resolution Data not available for 14 at 5000 resolution ........................

I got this error earlier also but it was resolved when I used v2.20.00 but couldn't run hiccupsdiff successfully this version, so I was looking for solutions.

— Reply to this email directly, view it on GitHubhttps://github.com/aidenlab/juicer/issues/312#issuecomment-1591792829, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AF63RA3OTQFSNOBIMU75S7DXLH777ANCNFSM6AAAAAAXTK6R2Y. You are receiving this because you commented.Message ID: @.***>

[varunkas]

Hi, so, I just ran into this issue (while running everything with juicertools 2.20.00). To reiterate, hiccups works and it generates the expected merged_loops.bedpe file. However, hiccupsdiff fails, with the following error:

$ java -jar juicer_tools.2.20.00.jar hiccupsdiff  DNMT3Amut55.allValidPairs.hic DNMT3Awtc13.allValidPairs.hic merged_loops.bedpe merged_loops.bedpe output/

....
Running HiCCUPS with alternate loop lists
Running HiCCUPS for resolution 10000
Data not available for chr1 at 10000 resolution
Data not available for chr2 at 10000 resolution
Data not available for chr3 at 10000 resolution
......
HiCCUPS complete
File output/file1/requested_list_10000.bedpe could not be parsed
File output/file2/requested_list_10000.bedpe could not be parsed

I will try the suggestion by @erikpark and update my findings. Thanks in the meanwhile.

Can the developers respond, please?

[varunkas]

Dear @erikpark,

I am running into the same issue that @rahulk87 faced, I think. With juicertools 1.19.02, the hicpro2juicebox.sh generates a .hic file. But hiccups does work on it. I am now trying regenerating the .hic file using the -r (restriction fragment) argument in the hicpro2juicebox.sh script.

In comparison with juicertools 2.20.00, hiccups works, but hiccups diff does not work.

Thanks in advance for any suggestions.

[varunkas]

A quick, happy update:

Turns out that all my issues were related to not using the right the right normalization string in the "-k" option. For example, using "-k SCALE" for *.hic files generated using juicertools.2.20.00 works all the way through to hiccupsdiff.