Following tutorial and the Splicing won't convert

[hope26]

Hello,

I have a research paper due tomorrow and my lecturer has been completely unavailable by email all weekend.

I have been attempting to turn some data from tabular to interval datasets, however, it keeps getting stuck in the orange loading phase for over 2 hours.

I don’t know what to do or how to fix this, can anybody help?

I have attached a link to the tutorial
https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html

[jennaj]

Welcome @hope26

We can try to help you to complete the tutorial. Would you like to share back your history so we can see the step where you are stuck? How to generate and post back the share link is in the banner of this forum, also here →

@jennaj

How to get faster help with your question

We love details! Consider Sharing your History or posting screenshots of your Job Information Details page.

Please confirm the Server URL (your web browser at the top!) and any Tutorial links involved.

We can also double check that this is working at the history where you are working. The public Galaxy server’s listed on the tutorial under Available at these Galaxies are usually the best choices, although it may work other places.

Then for your specific issue mentioned.

@hope26

I have been attempting to turn some data from tabular to interval datasets, however, it keeps getting stuck in the orange loading phase for over 2 hours.

The yellow/orange dataset color indicates that a job is still processing. Depending on the tool, this can be very normal. If you are just converting the datatype, this should go quickly, but if you are executing a tool, that can run at a variable time limit, up to several days in some cases.

@jennaj

When working at UseGalaxy.org, UseGalaxy.eu, or UseGalaxy.org.au, your analysis jobs execute at large scale academic clusters. Hundreds of thousands of jobs process each month!

• Use a Workflow for batch work.
• Allow queued (grey color) and executing (yellow-orange) datasets 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 (especially for ‘big’ jobs, e.g. alignments).

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Let’s start there! Seeing your history would be the best way for us to help more.

[jennaj]

Hello again @hope26

We didn’t hear back, so hopefully you have been able to work your way through the tutorial successfully!

As a small test, I ran the tutorial’s inputs through the included workflow at the UseGalaxy.eu server yesterday, and that has finished successfully. Maybe this reference helps but we can also follow up with your “Hand’s On” run through.

• Tutorial → Hands-on: Genome-wide alternative splicing analysis / Genome-wide alternative splicing analysis / Transcriptomics
• Workflow → Workflows / Genome-wide alternative splicing analysis / Transcriptomics
• Workflow Invocation → https://usegalaxy.eu/workflows/invocations/1628fb3e2effc661
• History → https://usegalaxy.eu/u/jenj/h/gtn-differential-isoform-expression-1

You should be able to navigate through these to see how the data was processed, or even import a copy to explore closer.