Histogram Rscript Error

[camtelope]

I want to plot kmer coverage using the histogram plotting script provided. However, I am getting an odd error I am unable to troubleshoot. I have been able to kmerize this file and run other options this program provides successfully.

My commands used go as followed:
dsk -file s_dys/fasta/GCF_000013425.1_ASM1342v1_genomic.fna.gz -kmer-size 31 -histo 1 -out outputfile

Rscript dsk/utils/plot-histo.R outputfile.histo

Error:
Error in bitmap(png.file, "png256", width = 7, height = 6, res = 300) :
GhostScript was not found
Execution halted

Any suggestions? Thanks in advance

[clemaitre]

Hi,

This issue comes from the bitmap function, used to save the figure in a png file, which requires Ghostscript to be installed on your machine. If Ghostscript is not installed, you can replace the bitmap function by png, jpegof pdf functions (modify the single line of code in plot-histo.R that calls bitmap()).
See for instance : https://search.r-project.org/R/refmans/grDevices/html/png.html

Best,
Claire