Job Stuck in Queue

usegalaxy.org support
, ,
#1

Hello,

I started a job last night around 8p CST and it is still stuck in queue now at 9:04a CST. I have run this pipeline before and have never had this happen. Is there something up on the server side or is there a way I can troubleshoot that isn’t listed?

tool: Maker Annotation Pipeline
total history data size: 1.18 GB (across 5 datasets)

Thanks!

1 Like
DNA seq paired-end read collection running slow (taking days)
#2

Hi @jxcronay

The https://usegalaxy.org server is very busy. While usually job queue times can be up to 24 hours, it is a bit longer right now. Give it 48 hours then let us know if you are still having a problem. If you write back, please confirm that you are working at https://usegalaxy.org – or share the URL of the server where you are working.

Other tips:

  1. How long jobs queue depends on the tool, the processing resource (cluster), how many other people are also running jobs that utilize the same processing resource, and how many other large jobs you personally have running.

  2. Problems with the inputs can also lead to stalled jobs. Review the inputs to the tool and confirm that are all intact, without errors/paused status, and are still active or hidden (not deleted). If you are using dataset collections, you’ll need to click into the collection to review the datasets inside of it.

FAQ: Datasets and how jobs execute

Thanks!

1 Like
#3

Hi @jennaj,

Thank you so much for your response. I did verify that the inputs are all correct and active. I am using usegalaxy.org and the Galaxy Tool ID is: toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10+galaxy1. For resources, I am using TACC Stampede2 (beta). I will give it an additional 24 hours and let you know if the job is still queued up.

Thanks again!

1 Like
#4

Hi @jennaj,

So the job ended up running for a short period of time, completed with no errors but yielded an empty output stating ‘0 lines’. (This was 2 days ago.) I started up the job again immediately, double checking all of my inputs (they were correct) and it has now been almost 48 hours and the job is still queued.

Same specs for usegalaxy dot org:

tool: Maker Annotation Pipeline
tool ID: toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10+galaxy1
total history data size: 1.18 GB (across 5 datasets)

Thanks again for all of your help!

1 Like
#5

Hi @jxcronay

I’m sending you a direct message. We’d like to help more directly.

Thanks!