Can I turn off my computer during Megablast In Galaxy?

Question: Can I turn off my computer during Megablast In Galaxy?

2.7 years ago by

Hi,

I just received my first Fastq files and I am using Megablast in galaxy for the first time. It seems that it will take a long time, as the job is still in grey (I understand that it has been queued?) What happens if I close my Galaxy session, or turn my cpu off? Will the job be performed or will have I to login again in Galaxy to allow the job being performed? How long is used to last a Megablast analysis (I have still around 100 000 reads after I removed low quality reads).

Thank you!

Etienne

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modified 2.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.7 years ago by etiennewalex • 30

2.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Etienne,

Create or log into your Galaxy account under the User top masthead menu. Creation or logging in, while this history is still active, will place the current history into your account. Then you can exit or log out and come back later. All histories will be saved automatically and can be found through the history menu option "Saved Histories".

If needed:

The job is indeed queued. Allow it to execute. The wait can vary. More: https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

Welcome to Galaxy! Jen, Galaxy team

ADD COMMENT • link modified 2.7 years ago • written 2.7 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you,

Actually, the history is into my account. I am not sure I understood well: the job can run even if I am logged out or do I have to be logged in to allow the run to execute once it is queued? I just logged in again and the job is still waiting to run. Does it mean that every time I log out it goes back in the queue?

ADD REPLY • link written 2.7 years ago by etiennewalex • 30

The original job will execute as initially queued and run when cluster resources are available, whether you are logged in or not. If still queued now (grey), then the server is busy or you have other prior queued jobs that will execute first. Hope this helps!

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by Jennifer Hillman Jackson ♦ 25k

Sure, thank you very much! So the server is busy because it is my only job queued. I hope it will run. I read elsewhere that if it does not finish into 72h the job will be cancelled.

Best

Etienne

ADD REPLY • link written 2.7 years ago by etiennewalex • 30

Dear Jen,

MEGABAST executed well. However, now I can't find how I can retrieve organism names as Megablast gives me only GI numbers. 2 months ago I was said to use Fetch taxonomic reprentation tool during a Workshop on metagenomic analyzes, but I can't find this tool now. What is the way do do this?

Thank you!

Etienne

ADD REPLY • link written 2.7 years ago by etiennewalex • 30

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