Question: Need help with "Map with Bowtie for Illumina" tool
gravatar for ghliu83
4.5 years ago by
United States
ghliu830 wrote:

How long will "This job is waiting to run" take?


Tool name: Map with Bowtie for Illumina
Tool version: 1.1.2
Tool ID:
ToolShed URL:


ADD COMMENTlink modified 4.5 years ago by Dannon Baker3.7k • written 4.5 years ago by ghliu830
gravatar for Dannon Baker
4.5 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

"Job is waiting to run" means that it's in the current queue and will stay there until it has been run (successfully or not) or has been deleted (cancelled).

There isn't a (good) way to guess how long a program (or those programs ahead of it in line) will take to run -- my best advice is to be patient as sometimes the queue can be long.

ADD COMMENTlink written 4.5 years ago by Dannon Baker3.7k


I just wanted to add that it is really important to not delete/restart jobs, in hopes that they will go quicker. Instead, just queue up jobs and permit them to run to completion - patience, as Dannon advises, is the best path. As is staging the next jobs in your analysis (when possible) now, by either adding in the next jobs or using a workflow (will queue up all your jobs at once, but each still execute in order).

When the server is busy, a good strategy is to try to start the jobs you care most about first (if working in multiple histories, or with multiple analysis threads in the same history). Jobs execute in the order submitted/started, per queue. There are a few different queues for different types of jobs. The queue that runs mapping tool jobs (and most other tools from the groups starting with an "NGS") has the largest cluster nodes, but also tends to be the busiest.

If it for some reason it seems that jobs are any state for a very long time (many hours, or sometimes an entire day), please be aware of the history "refresh" function. (For example, a "yellow" executing job may appear to be running when it is actually finished - I miss this myself sometimes!). There is a "double arrow circle" above the history panel - give it a click once in a while (but not too often!) to make sure that the view is current. Sometimes when a browser is open for a while without any actions performed, the history panel contents can become stale. This action will reveal the true job status.

This wiki has more about dataset status, what those look like the web interface, and how those indicate job progress:
And the wiki for the public Main server at explains how much job quota each account has:

If you are not working on Main, then the owner of the other Public Galaxy likely posts quota information somewhere on or linked from their site, or will provide it if contacted.

Best! Jen, Galaxy team

ADD REPLYlink written 4.5 years ago by Jennifer Hillman Jackson25k
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