Flat Average Profile Plot

[mmYeung]

I have been running ngsplot on the Unix cluster at my research institute and we have found that ngsplot(version 2.63) generates flat average profile plots, whilst ngsplot(version 2.61) generates the expected profile over the given bed file. As such, I'm wondering what may have caused this issue?

The bed file specified in the config file is the summit.bed file generated by peak calling with macs2.

The command used to generate these plots is:
ngs.plot.r -G hg19 -R bed -C config.txt -L 5000 -O peaksPlot

I have attached a copy of the average profile plots, as generated by versions 2.63 and 2.61, the BAM file header (which is consistent across the 3 bams to be plotted), a snippet of the summits.bed and the format of the config file.

cluster_ngsplot2.63.pdf
cluster_ngsplot2.61.pdf
bam_header.txt
config.txt
bed_snippet.txt