I understand that Shovill has an option under “Advanced Options” for “Post-Assembly Correction.” If this function is enabled (default is off), can I assume that Shovill will map the reads back to the reference contigs (via BWA-MEM2 or Bowtie2) and then run Pilon for correction? Additionally, how many rounds of Pilon correction are performed?
I attempted to run Shovill, but it appears to be stalling. Could I confirm if we receive log statistics or output files for the BWA-MEM2/Bowtie2 alignment as well as for the Pilon correction?
How the tool works in Galaxy is exactly the same as it works everywhere else. That means the original usage guides are the best reference for exact answers about the algorithm. Start here, since I think the top level is addressing your questions with brevity.
Then, for your stalled job, do you mean that the assembly is still running (yellow dataset)? That sounds normal. Assembly is computationally demanding, so it takes some time to complete. Allow jobs to finish or you won’t get any logs at the end. This tool will produce useful logs for any job (advanced settings or not) even if it fails. You want those logs! It can help to tune the runtime parameters for the next job you try. Find the logs under the i-icon.
More about how jobs work is here:
Hope this helps and if you need help understanding what happened after your job completes, please come back and we can try to help more. How to share your work is in the banner at this forum and is usually needed for actionable advice.
