Hi
I am trying to map my paired-end scRNA-seq data using bowtie2 on Galaxy but it keeps saying job is waiting to run. How long does it usually take for it to run?
Please help.
Hello,
Tools will run when resources are available at most Galaxy servers. This can take up to a day at Galaxy Main https://usegalaxy.org yet is usually much quicker. This depends a bit on how busy the server is, the type of job, how many were queued by the same end-user -- please see the FAQ below for more details about how Galaxy Main allocates resources in a fair manner for everyone.
It is important to not delete and rerun unless there is an input/parameter problem that you need to change. Rerun jobs, just like new jobs, are placed back at end of the server's job queue again. In practical terms, an exact rerun extends wait time for jobs that were already in the queue. Even if a server issue is discovered later on (there are none right now for Galaxy Main), queued jobs retain their placement and our administrator will resume them in queued order if left intact, plus you'll get results quicker. If an actual rerun is required (rare), review recent posts and ask if it is not already posted, and we can let you know.
That said, should any particular tool take longer than a day to execute, please let us know.
Note: A "queued job" is distinct from a "paused job" (grey versus blue). Paused jobs indicate that there is a problem with the inputs -- check the upstream jobs/inputs and make sure they were successful. You can correct the problems and resume downstream tool execution in many cases. Ask if you need help after reviewing the tool-error troubleshooting FAQ below.
FAQs: https://galaxyproject.org/support/
Thanks! This question is asked frequently, so I wanted to give a current update about how to interpret/act if a job is delayed.
Best, Jen, Galaxy team
