dims do not match the length of object when running ARA

[chenggang108]

Hi

I run into some problems when Aggregate Region Analysis (ARA). This situation is a little weird. Hope you can help with it.

First, I have several .mcool files from different cell stages, that are generated through the same pipeline. The files are loaded by the same way. Most of the files show this error. But some of the files can go through.

Second, when I load the files with different resolution, the lower resolution can go through(100k), the higher resolution showed this error.

Could you please help with this issue?

Thanks

Gang

[robinweide]

Hi Gang,

It's hard to troubleshoot from what you have written (we highly recommend reprexes).

Do you get the error when loading (i.e., do you get valid contact_objects), or when you try to run ARA? If it's the latter, my first guess would be that you are running out of memory. High-resolution/large-dataset ARA is very intensive in that regard. Try the following for troubleshooting:

• Limit the number of samples to ARA to one by one: you can always combine them later.
• Limit the number of region-entries to one chromosome.
• When running, keep an eye on your memory (on Mac use Activity Monitor; on Linux use htop).

Best, Robin

[chenggang108]

Thank you Robin,

The sample is loaded correctly. Because I can do the other analysis, such as RCP. The problem is ARA. I will try run it with one chromosome and see what will happen.

Best

Gang