cannot open the connection

[newpest]

rdo = new("rdObject") Error in { : task 1 failed - "cannot open the connection" In addition: There were 24 warnings (use warnings() to see them)

[chrisamiller]

That generally means it can't find the files it's looking for. Make sure you've set up your input directories correctly

[newpest]

my directories: params

annotations: entrypoints gcWinds mapability

output:

reads: chr1.bed

[newpest]

In my working directory, I can successfully read the parameter file：

> getwd()
[1] "/readDepth"
> read.table("params")
               V1   V2
1      readLength  100
2             fdr 0.05
3  overDispersion    1
4    gcWindowSize  100
5      percCNGain 0.05
6      percCNLoss 0.05
7       chunkSize  1e7
8        maxCores   16
9       readCores   16
10        verbose TRUE

[chrisamiller]

In addition: There were 24 warnings (use warnings() to see them)

Did you use warnings() to get details of the problems? Do your inputs and data all match?