#1 Excavator2 module 3 error JointSegIn

[Marc Pauper]

Hello, and thanks for sharing this tool!

I am trying to run the third and last module, in pooling mode.
The program quickly ends with an error:

Error in JointSegIn(DataSeq1, muk, mi, smu, sepsilon, Pos1, omega, eta,  :
  NA/NaN/Inf in foreign function call (arg 3)
Calls: JointSegIn -> .Fortran
Execution halted

[Alberto Magi]

Hi,

this error comes when there's inconsistency with the target you have used. It's likely that the bed file contains overlapping bases that are not allowed.
Please check and correct it and then rerun EXCAVATOR2 from scratch.

[pradyumna J]

merge the overlaping bases with

sort -k1,1 -k2,2n *.bed | bedtools merge 

[Lihi]

Hello,
I keep getting the same error eventhough I sorted the bed file as suggested above. any other suggestions? I ran it in paired mode.
thx

[Vivian Chu]

Hi, I have a similar error to the one mentioned above. I merged the bed file using your command but after running it from scratch again, I also still get the same error with JointSeg.

[Lihi]