Datasets and how jobs execute: How to interpret gray datasets with a "This job is waiting to run" message

jobs
queued-gray-datasets
#1

I’ve been trying to upload 59 fastq.gz files, each around 500 MB. These are going into a new history, and I uploaded them from disk with Type = “fastq.gz” and Genome = “S. cerevisiae”. In the upload pop-up window, the files were successfully uploaded. However, when I close the window and view this history, only 40 out of 59 are “green”, while 19 are grey and are flagged “this job is waiting to run”.

I’ve waited 6 hours, and on occasion one more file gets processed. I’m not sure what is being processed to begin with, or why it is taking so long? I’m confused as to what is even being performed, as this was just an upload (which showed completed?) - not sure what is being processed here?

I’ve tried refreshing, and resuming the jobs. I also tried deleting the history and starting over fresh - this didn’t work.

Thanks for any help!!

1 Like
#2

Hi @JVGen!

Queued jobs should be left in the queued state. These will eventually finish.

This includes Upload jobs. Metadata checks and assignments are made during this process that moves loaded data into a history. This is usually quick, and sometimes not – much depends on the overall server load and a few other technical factors.

Starting over or rerunning jobs will only result in those new jobs being added back at the end of the queue, extending the wait time.

The public server Galaxy Main https://usegalaxy.org has had more windows of extended wait times than usual over the last few days. We are actively monitoring the ongoing rates of job processing.

FAQ: Datasets and how jobs execute

Thanks for reporting the issue.