Memory error

[Nohaosma]

Hi,

I am using TopDom software to detect TADs from human chromosomes. it works perfectly with smaller chromosomes such as 22 and 21 but when I tried to use it for chr1, I got this error.

[1] "#########################################################################"
[1] "Step 0 : File Read "
[1] "#########################################################################"
[1] "-- Done!"
[1] "Step 0 : Done !!"
[1] "#########################################################################"
[1] "Step 1 : Generating binSignals by computing bin-level contact frequencies"
[1] "#########################################################################"
[1] "Step 1 Running Time : 0.697000000000116"
[1] "Step 1 : Done !!"
[1] "#########################################################################"
[1] "Step 2 : Detect TD boundaries based on binSignals"
[1] "#########################################################################"
[1] "Process Regions from 1 to 48609"
[1] "Step 2 Running Time : 1.96800000000007"
[1] "Step 2 : Done !!"
[1] "#########################################################################"
[1] "Step 3 : Statistical Filtering of false positive TD boundaries"
[1] "#########################################################################"
[1] "-- Matrix Scaling...."
Error in seq.default(1 + (n_bins * i), n_bins * n_bins, 1 + n_bins) :
'to' must be a finite number
Calls: TopDom -> scale -> seq -> seq.default
In addition: Warning message:
In n_bins * n_bins : NAs produced by integer overflow
Execution halted

Please could you help to figure out that issue?
Thanks

[Rseq]

Hi,
I had the same error. It also reported:

Warning message:                                                                                                                                                        
system call failed: Cannot allocate memory

However, I don't believe it is memory - I have 500Gb RAM.
Are you using the whole genome?
Have you figured out or just move to another TAD caller?

Best

[JSegueni]

Hey @Nohaosma,
I also faced this issue and have posted a solution to overcome it, here: https://github.com/JSegueni/TopDom
Hopefully, this can help.
Best,
Julie.