# Shovill and Pilon correction

**URL:** <https://help.galaxyproject.org/t/shovill-and-pilon-correction/13871>\
**Category:** usegalaxy.eu support\
**Tags:** tool-help, shovill\
**Created:** [November 11, 2024, 2:26pm UTC](https://help.galaxyproject.org/t/shovill-and-pilon-correction/13871 "2024-11-11T14:26:27Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![zschong](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/zschong/32/1886_2.png) [@zschong](https://help.galaxyproject.org/u/zschong)\
**Post date:** [November 11, 2024, 2:26pm UTC](https://help.galaxyproject.org/t/shovill-and-pilon-correction/13871/1 "2024-11-11T14:26:27Z")

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Hi all,

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?

Thank you

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [November 12, 2024, 12:33am UTC](https://help.galaxyproject.org/t/shovill-and-pilon-correction/13871/2 "2024-11-12T00:33:13Z")

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Hi @zschong

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.

- [GitHub - tseemann/shovill: ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads](https://github.com/tseemann/shovill)

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](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_icons.html).

More about how jobs work is here:

> [@Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1):
>
> ⏰ When working at [UseGalaxy.org](http://UseGalaxy.org), [UseGalaxy.eu](http://UseGalaxy.eu), or [UseGalaxy.org.au](http://UseGalaxy.org.au), your analysis jobs execute [at large scale academic clusters](https://training.galaxyproject.org/training-material/faqs/galaxy/#analysis). Hundreds of thousands of jobs process each month!
> 
> - Use a [Workflow](https://training.galaxyproject.org/training-material/search2?query=workflow) for batch work.
> - Allow [queued (grey color) and executing (yellow-orange) datasets](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_job_status.html) to finish processing.
> - Deleting and rerunning puts your job back _at the end_ of the queue again!
> - Job priority is the exactly the same for everyone.
> - **Be patient**. Galaxy is a free service, when a lot of people are using it, [you may have to wait longer than usual](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_jobs_not_running.html) (especially for ‘big’ jobs, e.g. alignments).

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. 🧑‍🔬