Long time for Goseq tool

I ran Goseq yesterday and still waiting for result. is it normal or else ?

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hi @amir

I suggest allowing the tool to complete. Runtime depends on the inputs and parameters used. The tool authors state that one of the initial steps for RNA-seq data processing is quote “computationally expensive”. Meaning, it takes both time (and sufficient memory) to complete that sub-step.


In general, how long a tool takes to run is always dependent on a few factors, whether run in Galaxy or not: Input size/content, parameters, and how the tool runs line command, plus allocated resources. Additional factors that are influenced by Galaxy are the allocated resources on whatever Galaxy server you are using, how busy that server is in general, cluster queues, and how many other jobs you have running (concurrent job execution quotas).

I know that you know this, but I’m including it for others reading: It is almost never a good idea to stop/restart a job once it has been submitted. The exception would be if you already recognize some problem with the inputs/parameters and need to fix or change something. Exact reruns only result in more delays – loss of queue position (if the job is still “gray” and queued) and loss of whatever processing has already been completed (if the job is “yellow” and executing).

If the job later fails, review the job details, inputs, stdout/stderr, usage help, and if you cannot figure out the problem, submit a bug report from the error dataset the Galaxy EU team through the web interface. Or, you can post the details back here and we can try troubleshooting – it depends on how much information the bug details contain.


cc @bjoern.gruening @hxr