How to force pilon to correct a reference with low coverage mapped reads?
Pilon will not consider fragments that are not proper pairs if the --frags option is used to pass the alignment .bam file. The reads mapped in the above IGV screenshot are unpaired.

Instead, if you want Pilon to consider all reads that map as legitimate and usable for correction, pass the .bam file with the --unpaired option instead.

To above corrected example would be:

java -Xmx100G -jar {params.pilon}\
  --genome {input.ref}\
  --unpaired {input.bam}\
  --output {params.outname}\
  --changes --fix all,amb,breaks,bases\
  --threads {threads}\
  --mindepth 1