# Why to consider Shovill instead of SPADes **URL:** \ **Category:** usegalaxy.org support\ **Tags:** assembly, spades, shovill\ **Created:** [February 26, 2025, 7:49pm UTC](https://help.galaxyproject.org/t/why-to-consider-shovill-instead-of-spades/14863 "2025-02-26T19:49:46Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Jennifer\_Kerr](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennifer_kerr/32/6853_2.png) [@Jennifer\_Kerr](https://help.galaxyproject.org/u/Jennifer_Kerr)\ **Post date:** [February 26, 2025, 7:49pm UTC](https://help.galaxyproject.org/t/why-to-consider-shovill-instead-of-spades/14863/1 "2025-02-26T19:49:47Z")
history: [https://usegalaxy.org/u/jkerr/h/srr26975044-illumina-c-elegans-spain](https://usegalaxy.org/u/jkerr/h/srr26975044-illumina-c-elegans-spain) I tried running a workflow with shovil and shovil alone. Both showed a fatal error with illumina dataset from SRA download ---
**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:** [February 26, 2025, 11:45pm UTC](https://help.galaxyproject.org/t/why-to-consider-shovill-instead-of-spades/14863/2 "2025-02-26T23:45:15Z")
Hello @Jennifer_Kerr I really like this assembler since the logs are so detailed! This is what is reported at the end of the `stdout` for one of your failed jobs. > [shovill] Assembly failed - spades.fasta has zero contigs! Find all job logs for datasets [using the i-info icon](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_icons.html) in any dataset (failed or successful!). ![Screen Shot 2025-02-26 at 3.31.28 PM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/7/7d0c747d22a938872cc48b898433e8861655c565.png) The read QA appears to have gone well, so the problem is likely with the parameters used. It appears that the current runs applied all or mostly defaults. Using the User guide as a reference. - [GitHub - tseemann/shovill: ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads](https://github.com/tseemann/shovill) It looks like [these reads](https://www.ncbi.nlm.nih.gov/sra/SRX22668488) were expected to have a coverge depth of about `30x`, so you could reduce the coverage to that range, or a bit larger like `50x`. This would prevent any potential pileup problems that might result from the higher 100x default. You could also specify the expected genome length. Yeast is about 100 Mb, so `100m` is a good value to start with. **Shovill** is using shorter (bacterial) plasmid lengths by default. We don’t have any other reports of technical problems with this tool right now, but I started up a test anyway applying the 50x-100m parameter set to see what happens. I would expect this to work unless there is something else special about these reads that wasn’t revealed during QA, or if there is potentially some new tool issue at the ORG server we need to address. - [https://usegalaxy.org/u/jen-galaxyproject/h/copy-of-srr26975044-illumina-c-elegans-spain-https-help-galaxyproject-org-t-fatal-error-running-shovil-14863](https://usegalaxy.org/u/jen-galaxyproject/h/copy-of-srr26975044-illumina-c-elegans-spain-https-help-galaxyproject-org-t-fatal-error-running-shovil-14863) That will need to finish executing, but you don’t need to wait. You should also experiment and we can follow up more here as needed. Hope this helps! 🙂 ---
**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:** [February 27, 2025, 5:34pm UTC](https://help.galaxyproject.org/t/why-to-consider-shovill-instead-of-spades/14863/3 "2025-02-27T17:34:27Z")
Update Hi @Jennifer_Kerr There is a server issue with your job, and it is impacting several job types. We are actively working to resolve this. I want to work with you to resolve this error specifically. I have another rerun processing to see how it will work out and will continue with technical tests until resolved. Thank you again for sharing your history with the example! More soon. More details at → [Notice at UseGalaxy.org Feb 27 2025: We are currently experiencing errors and delays](https://help.galaxyproject.org/t/notice-at-usegalaxy-org-feb-27-2025-we-are-currently-experiencing-errors-and-delays/14874) ---
**Author:** ![Jennifer\_Kerr](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennifer_kerr/32/6853_2.png) [@Jennifer\_Kerr](https://help.galaxyproject.org/u/Jennifer_Kerr)\ **Post date:** [February 27, 2025, 6:26pm UTC](https://help.galaxyproject.org/t/why-to-consider-shovill-instead-of-spades/14863/4 "2025-02-27T18:26:45Z")
thanks so much for the update. I appreciate it. When I initially posted, I had also ran the same workflow and Shovill on other data. It was from the same SRA project and showed the same failure message (one additional example: [Galaxy](https://usegalaxy.org/u/jkerr/h/srr26975042-illumina-c-elegans-bristol)) I am going to try downloading a previous SRA dataset that was successful using Shovill and try that as well. ---
**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:** [March 1, 2025, 12:56am UTC](https://help.galaxyproject.org/t/why-to-consider-shovill-instead-of-spades/14863/5 "2025-03-01T00:56:12Z")
Hi @Jennifer_Kerr Ok – I think this is working now! My last test is in the same history I shared above. It is still running but I would have expected it to fail by now, and I’d like you get you a solution before the weekend. There was a configuration problem on our side, and we think that has been adjusted. I would still recommend setting the assembly parameters to fit the data but the memory allocation should at least be corrected now. Thank you so much for follow up! Any problems, please let us know, and we can continue this topic next week until actually resolved! 🙂 ---
**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:** [April 14, 2026, 7:38pm UTC](https://help.galaxyproject.org/t/why-to-consider-shovill-instead-of-spades/14863/6 "2026-04-14T19:38:08Z")