DEseq2 has been running for almost 3Days now !

Is there any issue with DEseq2 ? I have been doing some RNA seq analysis for DE genes in treated samples with two replicate each for two conditions but it seems to take long time…is it usual? Its my 1st time with the tool…

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I have been running my analysis with 30 million reads of RNAseq data ! how much runtime does DEseq2 generally takes for this amount of data ?

Thanks Already ! Wish you all Good Health in the worst of times ! :slight_smile:

Hi @Hart95

Has the job been queued for a long time (gray dataset)? That may be possible. The server is very busy. The best strategy is almost always to allow queued jobs to stay queued. If you delete and restart them, they just move back to the end of the queue again, extending the wait.

No job should actually be executing (yellow/peach dataset) for over 3 days – that would exceed the maximum “walltime” (runtime) on the clusters at Galaxy Main https://usegalaxy.org.

The runtime for executing jobs varies not only by the number of reads, but the reference genome and parameters used (among other factors). If a job is already executing, allow it to complete unless you already know something is wrong with it (problematic inputs, settings, etc). Certain types of input problems can cause jobs to run out to their maximum memory or runtime usage – and that can be quick or long (few days, once not queued anymore) – then they eventually fail (red error result).

Help for using DE tools, including links to Tutorials, is here:

General troubleshooting, including info about how to interpret jobs that fail for resources (memory or walltime):

Thank you! You too.

Let us know if you need more help. Thanks!

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The thing is the dataset didnt turn red or grey anytime in this week it has been 5 Days now, i have run the analysis on 23rd April 2020 and its still running…

Can you let me know something why the wall time for JETSTREAM server is being reduced from “N” to 48 hrs? Is it gonna be like that way here after?

Hi @Hart95

All jobs start out as grey originally. You may have missed that step (job started to execute, moving to a yellow/peach color).
https://galaxyproject.org/support/how-jobs-execute/

Jetstream usually has a walltime of 36 hrs.
https://galaxyproject.org/main/#choosing-computational-resources

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