Java issues (resolved) and file.hic issues (new)

[Alexis Egea]

Hi again everyone,

So, i solved my issue concerning java problems thanks to some adjustments with Xmx and Xms.

So,

- Calculating norms was performed

- I have also the following message "Done creating .hic files"

- ARROWHEAD and HICCUPS running successfully.

- APA running until this "***!  Not running motif finder" but i thought it was not necessary right ?

- "(-: Feature annotation successfully completed (-: "

And now, i have this issue :

" ***! Error! Either inter.hic or inter_30.hic were not be created"

" Either inter.hic or inter_30.hic were not be created.  Check  for results"

==> So, i have .hic files and the last message don't show the folder so, i think all is good !

The main problem now is when i used .hic file with JuiceBox, i can't use them because the following error occurs : "error loading .hic file"

Can someone tell me why i have this issue and how can i solve this please ?

Thanks a lot for your help and have a nice day.

Alexis.

[Muhammad Shamim]

Are you able to load the files at aidenlab.org/juicebox?

If you used the latest Juicer 2 pipeline to build the .hic files, you'll need to use the latest Juicebox jar:

https://github.com/aidenlab/Juicebox/releases/tag/v.2.13.07

[Alexis Egea]

Hi,

First, thanks for the reply.

I don't have the file in my computer for now, i can check this in 2 days.

But i already used this link to download Juicebox https://github.com/aidenlab/Juicebox/releases/tag/v.2.13.07 when i want to test my files and i can't load my hic files ... maybe  aidenlab.org/juicebox will can allowed me to load my files ? 

I will check when i can with your first link ( aidenlab.org/juicebox ).

My objective was to used them for the data extraction, but i thought that if i can't load them in Juicebox, maybe they are incomplete for the analysis ? 

Thanks again for your reply.

Best regards,

Alexis.

[Alexis Egea]

Hi, 

It works perfectly with this link aidenlab.org/juicebox !

Thanks a lot for your help !

Have a nice day,

Alexis

[Levi Bauer]

Alexis,

Can you go into detail regarding how you resolved the  error regarding missing .hic files? I am currently having similar issues myself.

" ***! Error! Either inter.hic or inter_30.hic were not be created"

" Either inter.hic or inter_30.hic were not be created.  Check  for results"

[Nolan Ruffenach]

Hi,

I had the same issue and to be honest, i don't solve it but the problem is about the code or arguments.

Indeed, your message is "Check  for results" but, according to the source code, it was "Check $PATH for results" so, the problem is that the final script don't have the path because he's not print in the output.

So, just check if you have some issues before of this one and solve them. Otherwise, it's fine (just check if these files are present in the corresponding path/aligned).

Hope it will help you.

Have a nice day,

Nolan.