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HenrikBengtsson / TopDom

R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
https://cran.r-project.org/package=TopDom
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Memory error #15

Open Nohaosma opened 4 years ago

Nohaosma commented 4 years ago

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 commented 4 years ago

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 commented 2 years ago

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.