Can not get result using GM12878 .hic or .cool or matrix file

[hmamohit]

Hi,

I am trying to run the app using GM12878 insitu primary MAPQ 30 dataset from GEO. I used the provided mappability file MboI_hg19_10Kb_encodeBL_F_GC_M_FULL.txt.gz. I used juicer dump to produce the matrix file from .hic data.
and hicexplorer to get the .cool file. I am particularly interested if it could be run with .hic or .cool file at 10KB chr1 and chr6.

While using .cool or .txt matrix files the process killed automatically without any error saying Killed
While using .hic file, it throws an error after dump operation. Though it produces the output file with columns with NA. It says,

Error in if (abs(end - as.numeric(as.numeric(u[i, 2]))) == 0) { :
  missing value where TRUE/FALSE needed

Output

chr start end GSE63525_GM12878_insitu_primary_30_norm_cis GSE63525_GM12878_insitu_primary_30_neg_ln_pval GSE63525_GM12878_insitu_primary_30_indicator
chr1 820000 830000 1.0515 NA NA
chr1 840000 850000 0.5381 NA NA
chr1 850000 860000 0.3838 NA NA
chr1 860000 870000 0.4243 NA NA
chr1 870000 880000 0.4911 NA NA
....................................................

Here, I provided a sample script three of them,

library("FIREcaller")
setwd('/home/ubuntu/loop_analyzer/data/hub/firecaller/')
hic_file<- paste0('GSE63525_GM12878_insitu_primary_30.hic')
gb<-'hg19'
map_file<-'MboI_hg19_10Kb_encodeBL_F_GC_M_auto.txt.gz'
juicer_version <- '/home/ubuntu/loop_analyzer/data/hub/firecaller/juicer_1.22.01.jar'
FIREcaller(hic_file, gb, map_file, juicer_tools_version=juicer_version, binsize = 10000, upper_cis = 200000, normalized = FALSE, rm_mhc = TRUE, rm_EBL = TRUE, rm_perc = 0.25, dist = 'poisson', alpha = 0.05, plots = FALSE, diff_fires = FALSE)

If I did anything that is not compatible with this app input, like input HiC data or mappability file, could you please share details to get the correct one.

Could you please help me. Thank you.