Medaka not working on Assemble Genomes Public Workflow on Galaxy

Help
1

Please find attached my history. I was running some samples and none of them were able to load the medaka section of the workflow.

AB1 Combined parent sample: Galaxy

2

Hi Newhe,

  1. The error in your history (see below) suggests that the tool ran out of memory.
    Screenshot 2025-02-18 at 11.25.30 AM
    Screenshot 2025-02-18 at 11.25.30 AM1536×658 65.2 KB
  • Galaxy team was able to increase the memory for the medaka consensus pipeline tool.
  • I re-ran your workflow with updated memory and it worked, so go ahead and try re-running it yourself, as the tool with expanded memory should work now. Note, the tool took ~1.5 hours to complete.
  1. Of note, medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. Your sequencing data is PacBio data and does NOT need pre-processing by medaka.