Error: 1 not found in the file

[ganjingbo]

Hello, when I run the below script on my computer, I get this error: 'Error: 1 not found in the file'. How can I fix the problem?

########################################################
library(FLAMINGOr)
library(Matrix)
library(GenomicFeatures)
library("strawr")
library("parallel")
library("mgcv")

all_size <- getChromInfoFromUCSC("hg19")
chr_name='1'
chr_name = as.numeric(chr_name)
chr_size = all_size[chr_name,2]
chr_name <- paste0('chr',chr_name)
res = flamingo.main_func_large(hic_data_low='./SRR13238426.hic',
file_format='hic',
domain_res=1e7,frag_res=5e4,
chr_size=chr_size,
chr_name=chr_name,
normalization='KR',
downsampling_rates=0.75,
lambda=10,max_dist=0.01,nThread=4,n_row=30000)
#########################################################
Error: 1 not found in the file.
#########################################################

[JiaxinYangJX]

Thanks for using our software! The chromosome ID should be consistent with your hic file. I guess there is no chromosome "1" in your hic file. Could you try to check with that by:
strawr::straw('KR','./SRR13238426.hic','1','1',unit='BP',binsize=10000000)

In addition, we are currently collecting all the feedback and reorganizing our tools. We will release a more user-friendly version by next month.

[JiaxinYangJX]

Hi @ganjingbo
Thanks for using our tools!
We just released a lite version of FLAMINGO, which is faster, more memory-efficient, and more user-friendly. We fixed the majority of bugs and hope the new version could help. Below is the link.
https://github.com/JiaxinYangJX/FLAMINGOrLite