Issue when running mm10 using custom bed file

[saimukund20]

I uploaded my inputs to google drive. https://drive.google.com/drive/folders/1jJ2QvBTdKuUFfnQS6769IHGLSqXelcVB?usp=sharing

I tried running the ngsplot.r on my downsampled bam as a test using my custom bed file with the following command:

ngs.plot.r -G mm10 -R bed -E Analysis7/WGBS_Analysis3_dmrs.bed -C downsampled.bam -O out -T 45417_h3K27_tri -P 4 -L 10000

I dont get any errors but warnings. Here is the output i am getting:

Configuring variables...Done
Loading R libraries.....Done
Analyze bam files and calculate coverageWarning message:
In headerIndexBam(bam.list) :
Aligner for: downsampled.bam cannot be determined. Style of
standard SAM mapping score will be used. Would you mind submitting an issue
report to us on Github? This will benefit people using the same aligner.
..................................................................................Done
Plotting figures...Done
Saving results...Warning message:
In data.row.names(row.names, rowsi, i) :
some row.names duplicated: 2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271 [... truncated]
Done
Wrapping results up...Done
All done. Cheers!

The outputs seem to be empty. I have placed them also in the google drive folder.

I would appreciate your help in troubleshooting this error.

Attached are all the inputs and outputs for your verification
Archive.zip