I’m using galaxy .org and my jobs have been stuck in the “new / queued” state for more than 3 hours. Not a single job has started running.
What I’m running:
Filtlong on a collection of 128 Nanopore FASTQ files (fastqsanger), with --min_length 500 and --min_mean_q 8, all other options left at their defaults.
Seqtk seq (-A, force FASTA output) on the Filtlong output collection.
What I see:
All elements are gray. The job info shows “new: This is a new dataset and not all of its data are available yet. queued”.
No job is red (failed) or paused, and there are no error messages.
I launched the same run a second time and it is also stuck in the queue. I [cancelled the duplicate run / left both running].
My disk usage is [0% / 268.4 GB], so I don’t think quota is the cause.
Questions:
Is there a known issue with the queue or the cluster right now?
Could running a 128-element collection at once be affecting my priority? Would it be better to launch it in smaller batches?
I’m also experiencing issues with Filtlong. For me, I’m trying to run a concatenated dataset of 114 FASTQ files through filtlong but it has been stuck in “queued” for two hours. Although I cannot say with confidence, I’m pretty sure theres an outage with Filtlong (since all tools in Galaxy work with external resources). I don’t know when it will come back, but I’ve previously ran a lot of files through Filtlong and this is definitely abnormal.
Hope everything goes well and Filtlong works soon!
I am experiencing a problem with a Galaxy job that has remained queued for an unusually long time.
Job details:
Galaxy server:
Dataset ID: 11139
Tool: Join two Datasets (Galaxy Version 2.1.3)
Input datasets: 11137 and 11138
Job submitted: October 17, 2026
Current status: Queued — “This job is waiting to run.”
Both input datasets are successfully completed tabular files containing approximately 1.1 million rows each.
The job has remained queued without starting. I have refreshed the Galaxy history and checked the job information, but the status has not changed.
Could you please check whether there is a problem with the job scheduler or available computing resources? Should I continue waiting or resubmit the job?
For the queued-gray-datasets , there isn’t anything special happening at UseGalaxy.org right now. The usual advice about confirming your inputs and leaving queued work queued will apply.
Status: a few hours is still a very short queue! If work is queued longer than a day, then we can help with a review here.
The inputs, tool, parameters, and server can all matter for this. How to share your work with all of these details is in the banner topic, also here. → FAQ: Sharing your History
The inputs, tool, parameters, and server can all matter for this. How to share your work with all of these details is in the banner topic, also here. → 
