Shovill producing blank contig graph file: Use Galaxy Version 1.1.0+galaxy2

maria_rosa · February 19, 2026, 9:48am

Some of my students and I have tried running Shovill on multiple files, and it is currently producing a blank contig graph file. I have generated this file successfully in the past, so there may be an issue with the current version.

jennaj · February 19, 2026, 5:19pm

Welcome @maria_rosa

Thank you for reporting the issue! The UseGalaxy.eu server had some recent change applied to the job configurations. This tool may have been impacted. I’ll run some tests.

Another person just reported an issue with a different tool. These same questions would be good to clarify for this tool as well – but I’ll also be testing myself.

Switching to using the version that “works” correctly may also be a solution for you. All prior versions are always available and users can navigate between them!

More soon and I’ll also watch for your reply.

Blast is not returning taxonomy results

Would you be able to confirm a few items so I can look into this closer and get it reported?

Server: this was at UseGalaxy.eu correct? The server had some tools updated recently, so this will be part of the review.

Tool version: wrappers have a versioning. Find this is on the rerun forms at the top or review on the job details page (i-icon). My guess is that these data were run using different versions but let’s confirm so I can reproduce exactly.

Please capture these details and let us know. If you want to post back the job details views in a screenshot that would be Ok, or you can share the history with the runs, but I think just the core details above will be enough for this.

What to do: if you want to reproduce results, try using the tool version that has the taxonomy attached. See → FAQ: Changing the tool version

jennaj · February 19, 2026, 5:58pm

Update

I have enough details already and was able to quickly reproduce the problem! I’ll get this reported and update the topic here once done. Thank you again for reporting the issue and our apologies for the confusion it lead to during your class!

Details

Reporting

The current version is the one with the problem and can be avoided:

Avoid: Shovill Faster SPAdes assembly of Illumina reads( Galaxy Version 1.4.2+galaxy0)
Alternative: Faster SPAdes assembly of Illumina reads (Galaxy Version 1.1.0+galaxy2) → FAQ: Changing the tool version

Screenshot

maria_rosa · February 20, 2026, 9:06am

Thank you for your reply and for chasing this @jennaj. I will advise my students that they can use the older version in the meantime!

liz_wright · February 25, 2026, 6:32pm

Hi I am in a similar situation and am using the MRSA illumina tutorial with my biochemistry class: Same problem, blank contig graph file. For the record, I am on use galaxy org I will try running with earlier Shovill version to see if problem is resolved.

liz_wright · February 25, 2026, 7:01pm

Maria, I am having the same problem and I tried running an earlier version of Shovill as suggested. It did not proceed nicely (eternally grey) so I am now running Spades. Sometimes haste makes waste (see –> Shovill)

liz_wright · February 25, 2026, 7:29pm

One more comment, spAdes ran successfully (and quickly) and produced a good contig graph file. That said, I have never been able to run Bandage successfully within Galaxy so I opt for the Bandage GUI and this works perfectly on the contig graph file.

jennaj · February 25, 2026, 9:46pm

Hi @liz_wright

Glad you were able to get the primary tool working! The queued datasets are just a matter of timing, so I can’t help with that beyond suggesting to use the TIaaS service. (which I’m sure you know about!)

If you would like to share a small history with your example of what is not working, I’d like to try to troubleshoot. This can include communicating with the developers to smooth things out? Seeing the process from reads through to this step would be helpful. You can share the history back here or we can start up a direct message to share privately.