error in nb_results and trans analysis

Hi am trying to analyze some mouse data but in the near bait function i have this warning and i dont get results-counts for some of my data.

> nb_results=nearBaitAnalysis(my_obj,k=10)
[1] "Building adaptive windows..."
[1] "Normalizing counts..."
[1] "Generating synthetic samples...."
[1] "Parameter estimation....."
[1] "BED file of highest interacting domains for near the bait on the cis chromosome are saved in Mouse_4cker_083_2018/"
Warning message:
In as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) :
  restarting interrupted promise evaluation

cis analysis is working fine and also in trans analysis i have another warning :

[1] "Building adaptive windows..."
[1] "Normalizing counts..."
[1] "Generating synthetic samples...."
[1] "Parameter estimation....."

Iter: 1 fn: 327385.8451  Pars:  0.33333 0.33333 0.33333 0.50000 0.25000 0.25000 0.25000 0.50000 0.25000 0.25000 0.25000 0.50000 1.47581 0.32309 2.36130 0.02980 2.95163 0.08850
solnp--> Solution not reliable....Problem Inverting Hessian.
[1] "Warning: only 1 iteration. Using starting parameters"
[1] "BED file of highest interacting domains for trans chromosomes are saved in Mouse_4cker_083_2018/"
Warning message:
In p0 * vscale[(neq + 2):(nc + np + 1)] :
  longer object length is not a multiple of shorter object length

My object is like that :

my_obj = createR4CkerObjectFromFiles(files = c( "bedGraph_files/ESC_pcdhb19_1_aligned_chr.bedGraph",
                                                "bedGraph_files/ESC_pcdhb19_2_aligned_chr.bedGraph",
                                                "bedGraph_files/ESC_pcdhb19_3_aligned_chr.bedGraph",
                                                "bedGraph_files/iPSC_pcdhb19_1_aligned_chr.bedGraph",
                                                "bedGraph_files/iPSC_pcdhb19_2_aligned_chr.bedGraph",
                                                "bedGraph_files/iPSC_pcdhb19_3_aligned_chr.bedGraph"),
                                      bait_chr="chr18",
                                      bait_coord= 37483203,
                                      bait_name = "Pcdhb19",
                                      primary_enz = "AAGCTT",
                                      samples = c("ESC_pcdhb19_1", "ESC_pcdhb19_2", "ESC_pcdhb19_3", "iPSC_pcdhb19_1", "iPSC_pcdhb19_2", "iPSC_pcdhb19_3"),
                                      conditions = c("ESC","iPSC"),
                                      replicates = c(3,3),
                                      species = "mm",
                                      output_dir = "Mouse_4cker_083_2018",
                                      enz_file=enz_file)

All bedgraph data are created based on your directions in Readme and reference with reduce genome function .

BEst Dimitris

rr1859 / R.4Cker

error in nb_results and trans analysis #52