Dear Piotr,

Since you do not use a hybrid assembly I see no reason to use Unicycler. Download and use the Spades assembler locally that is anyway the assembler used by Unicycler. Like this you minimize the complexity of your problem. If Spades fail then you can easily see where and why and find a way to fix it. Personally I do not even trim anything and let Spades do error correction and quality filtering. The manual of the tool is very clear and it is easy to use so give it a try before you spend hours trying to debug a Unicycler.

Good luck,

Ilias

You should contact the Galaxy admin. If it isn't a Galaxy issue, then contact Unicycler developers through GitHub

https://github.com/rrwick/Unicycler

Are you able to download Unicycler and used it for your own?

Did you check if you exceed the capacity of Galaxy memory use?

On other hand, try to run any tool as convert fastq to fasta and check for contamination. If you have sequence error, it should be indicated running any tool otherwise the Unicycler might require some format or indexed genome or many other parameters you do not accomplish. The last possibility is tool bug in Galaxy itself, you should then contact the admin.

Hope it helps and let us know how you solve it.

Loub

Loubna, Xabier thank you for your responses.

there is some kind of issue with Unicycler tool @ https://usegalaxy.org.

https://github.com/galaxyproject/usegalaxy-playbook/issues/61

it seems that I should try to implement offline version of Unicycler.