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wangjr03 / FLAMINGO

MIT License
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Error: 1 not found in the file #14

Open ganjingbo opened 1 year ago

ganjingbo commented 1 year ago

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 commented 12 months ago

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 commented 7 months ago

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