I'm new to galaxy and am trying to use the cloudmap workflow to conduct "Hawaiian variant mapping with WGS data". The WGS data was initially provided as pair-end data in two files. I converted the files to fastq.sanger using the "groomer" tool then joined the two files together using the "joiner" tool. When I perform the Hawaiian variant mapping workflow. Everything seems to work fine but the "scatter plots" of the SNP ratios always fail. Any idea why this is happening? Is the WGS data in the correct format?
My "joined" pair-end reads look like this: