error loading .hic file

[vmukhina]

Hi, I am trying to visualize file (~450mb) generated with juicer 1.6. It works seamlessly in web version but in desktop version (Juicebox 1.9.0, mac M1) it keeps evoking 'error loading .hic file'. Test file downloaded from https://bcm.app.box.com/v/juicer-tools-testing as well as other random hic files produce no error but no visualization as well. I checked also ENCODE test files provided together with juicebox and there is no such problem. Can you please help me to understand what can be wrong with my local files? Thanks!

[dougbarrows]

Hello! I am having a very similar issue. I have .hic files that came from the NextFlow HiCAR pipeline (https://nf-co.re/hicar), and I am able to open them in the web version of juicebox, but I am getting an error in the Desktop version (v1.11.08). Other .hic files from ENCODE and various sources load fine into the desktop version as well. Any advice on how to debug this would be greatly appreciated - thank you!

[JohnUrban]

I'm also seeing this on Development Version (1.11.08) (https://github.com/aidenlab/Juicebox/wiki/Download) for Mac. The .hic file loads fine on the web (https://aidenlab.org/juicebox/), but gives the "error loading .hic file" message on the 1.11.08 Mac version.

Edit: I used the YAHS Hi-C pipeline, and generated the .hic file as they recommend here: https://github.com/c-zhou/yahs

BIN=../yahs.out.bin 
AGP=../yahs.out_scaffolds_final.agp 
FAI=../../../input/canu_primary.fasta.fai
ALN=alignments_sorted.txt
SCF=../yahs.out_scaffolds_final.fa
SZS=yahs.out_scaffolds_final.sizes
HIC=out.hic
JAR=/mnt/sequence/jurban/software/yahs/juicer_tools.2.20.00.jar

(juicer pre ${BIN} ${AGP} ${FAI} | sort -k2,2d -k6,6d -T ./ --parallel=8 -S32G | awk 'NF' > ${ALN}.part) ##&&
(mv ${ALN}.part ${ALN} )

faSize -detailed ${SCF} > ${SZS}

(java -jar -Xmx32G ${JAR} pre ${ALN} ${HIC}.part ${SZS} ) ##&&
(mv ${HIC}.part ${HIC})

[MahdiSayadSadr]

Hi,

Could you let me know if this problem persists in this version of Juicebox? https://www.dropbox.com/s/hfre4oqac5jirmh/Juicebox-2.15.dmg https://www.dropbox.com/s/okbqfaa82mswa3i/Juicebox-2.15.msi

[vmukhina]

Hi @MahdiSayadSadr Test file works well comparing to the previous version (there was no visualisation for this file). I switched to the cool* soft so can't test my original .hic files anymore, sorry.

[dougbarrows]

The files that did not work for the previous version of Juicebox are now working for me in this version. Thanks!

[JohnUrban]

@MahdiSayadSadr Juicebox-2.15 solved it for me (https://www.dropbox.com/s/hfre4oqac5jirmh/Juicebox-2.15.dmg). Thanks for sharing!