RepeatExplorer sampling less and less each run

Hi all,

I’m running RepeatExplorer for ~12 populations. Due to quota limitations, I upload only one population at a time, concatenate the sequences, and then have RepeatExplorer randomly sample 2,000,000 reads. The first run it sampled only 520,000, which I assumed was because it automatically downsamples to meet the reserved memory (4 Gb). However, each run after sampled less: 370,000, 200,000, 130,000, and 70,000. I understand that it may downsample due to the repetitiveness of the genome, but the last few have the smallest genomes and, at least according to the output, much lower repeat content.

Can someone explain why it appears to be behaving this way?



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Welcome @hancockzb

Are you using the public Galaxy server at If so, you should contact them directly for help regarding quotas or odd behavior. Details are in this prior topic: