lastz not running

Question: lastz not running

3.4 years ago by

United States

rooneyl • 0 wrote:

I want to align my reads to a short fasta file to determine how many reads I have that match my target gene of interest (CFTR). I am using LASTZ alignment in galaxy; however, after I convert .gz reads file to fasta format, trim the adapter sequence and upload the target sequence as a .fa the LASTZ just hangs and never completes and never indicates an error?

Besides refreshing the history what else can I try to get this application to run?

Sincerely,

LeeAnn

alignment galaxy • 1.0k views

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modified 3.4 years ago • written 3.4 years ago by rooneyl • 0

3.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If the job is grey, that means that it is in the queue to run. How long a job will queue depends on server/cluster load (all users) and how many other jobs you have running/queued from your account. Wait times can be up to a day for certain tools and at peak usage times sometimes longer (although, this is not common).

More about datasets UI cues (color coding and the like) is described in this wiki: Dataset_status_and_how_jobs_execute

If the job is small, you might want to consider using a local Galaxy. If interested, start here: http://getgalaxy.org

If larger, and time is a factor, moving to a cloud Galaxy is another choice. A full list of ways to use Galaxy is here: BigPicture/Choices

Best, Jen, Galaxy team

ADD COMMENT • link modified 3.4 years ago • written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer,

Thanks for your reply, I deleted runs (in grey) as well as tried to re-run. Is there anything I can do now to clean this up? As per comment below found on the sight you indicated in your email " Support - Galaxy Wiki"
Thanks Again!
LeeAnn

grey - the job is waiting to run
- If you are using the public Main<https: wiki.galaxyproject.org="" main=""> Galaxy instance, this job is queued, waiting for an opening on the appropriate cluster. It is very important to allow queued jobs to remain queued, and to not delete/re-run them. If re-run, this not only moves the new job back to the end of the queue, effectively lengthening the wait time to execute, but if done repeatedly, the volume of "executing deleted" jobs can create additional work processes in the history as these are cleared away, using up resources, and can cause additional delays.

ADD REPLY • link written 3.4 years ago by rooneyl • 0

Hi LeeAnn, Jobs in the queue run when there is resource available. Hopefully any started Friday are running or have completed by now. To recover space, you can permanently delete any jobs that you terminated. Jen

ADD REPLY • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer, So my LASTZ is still running four days later. I noticed on the Edit Attributes the following message " required metadata values are missing..." Can you tell me what is needed? Thanks, LeeAnn

From: Jennifer Hillman Jackson on Galaxy Biostar [notifications@biostars.org] Sent: Friday, July 17, 2015 11:13 AM To: LeeAnn Rooney Subject: [galaxy-biostar] A: lastz not running

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: lastz not running<http: biostar.usegalaxy.org="" p="" 13220="" #13222="">:

Hello,

More about datasets UI cues (color coding and the like) is described in this wiki: Dataset_status_and_how_jobs_execute<https: wiki.galaxyproject.org="" support#dataset_status_and_how_jobs_execute="">

If the job is small, you might want to consider using a local Galaxy. If interested, start here: http://getgalaxy.org

If larger, and time is a factor, moving a cloud Galaxy is another choice. A full list of ways to use Galaxy is here: BigPicture/Choices<https: wiki.galaxyproject.org="" bigpicture="" choices="">

Best, Jen, Galaxy team

ADD REPLY • link written 3.4 years ago by rooneyl • 0

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