eigen decomposition failed error

[yeroslaviz]

I am running the CALDER tools against several chromosomes of my data set. When I run CALDER against chr1 I get the needed output, but when I tried to run it against chr2 or chr10, I get the following error:

CALDER_main(contact_mat_file = "straw/1082/hic_chr2_5K.txt", chr = 2 , bin_size = 5000, out_dir = "CALDER_output/1082_5k", sub_domains=TRUE, save_intermediate_data=TRUE, genome='mm9')

>>>> Begin process contact matrix and compute correlation score at: 2022-06-24 11:19:33
 >>>> Begin compute compartment domains and their hierachy at: 2022-06-24 11:23:51Error in do.call(.Call, args = dot_call_args) :
  TridiagEigen: eigen decomposition failed
In addition: Warning message:
In cor(t(trend_mean)) : the standard deviation is zero

Any ideas, were this error is coming from or why it happens only at specific chromosomes?

thanks again

Assa

[YuanlongLiu]

Hi, it might be the matrix is too big and the eigen decomposition failed, refer to this (yixuan/RSpectra#1). One suggestion is to run the analysis at bin size >= 10kb. The sub-compartment call should be already quite precise

Also, take a look at CALDER2.0 with several updates