Hello,
im working on a Whole Genome Sequencing of my bacteria but i’m stuck with SPAdes. I’m stuck in queue since yesterday. Is there anything i could do to improve the workflow?
Thank you
Yannick
Welcome @yannick.fornoville
Job Queues
This looks like your job is queued. This is normal and expected when working at the public clusters! The best advice we have is to allow the job to move up in the queue and process. Deleting and rerunning will only put the job back at the end of the queue again.
As long as the inputs in the history are in a green dataset state, are not empty, and are the correct choice for the tool, the job will attempt to run. If it fails later, then you can review for content issues based on the error message.
It seems the UseGalaxy servers in general are very busy! This was a question from another user asking about SPADes a few days ago. The clusters will look about the same at all of the servers since many people work at all of them! → Jobs stuck overnight: assembly and mapping tools may queue!
Troubleshooting this specific job: inputs and parameters
For your specific job, we can see that datasets 72 and 73 are the “paired” outputs from Trimmomatic. However, SPADes now requires that paired end reads are first put into a collection folder, then QA is run on the collection, and finally the collection is input to the assembly tool. Now, older versions of SPADes will accept individual files, but I would expect that use case to have the dataset numbers listed in the reverse order in the output dataset name, so I still think there is some problem there.
This recent topic goes through what you should review. It involves the same tools, so your steps should look very close the recommended path here. → SPAdes: why and how to use intact Paired End reads, plus production workflows for Bacterial assembly! - #2 by jennaj
To see what you did for each step, click into your Job Information Details pages for each. You might be able to notice choices for single-end instead of paired-end and that is what you will be correcting.
From here, if there is a problem, you can delete the assembly job you don’t need, then start this up again. See the topic I linked for public workflows too! Even when creating your own, reviewing what others are doing can be helpful and these are the production versions. The GTN will have training versions with exact instructions, so be sure to review there as well if this is new to you!
Hope this helps and let us know how this turns out! You are welcome to share your history for more specific feedback. → FAQ: Sharing your History 