Workflow problems using galaxy

Question: Workflow problems using galaxy

2.6 years ago by

sverga • 0

sverga • 0 wrote:

I've tried to set up a workflow for differential expression analysis. i have set it up to place the data in a new history. I've waited set days now and cannot find any results. Additional, i havent been able to determine if the programs are still running.so I can't tell if there was an error that occurred in the process. I've set up the work flow to perform cufflinks, cuffmerg, and cuffcompare. Some insight into how to work galaxy would be appreciated. Thanks, Sam

rna-seq • 613 views

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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by sverga • 0

Hello,

Look under "Saved Histories" to locate the workflow's target history and datasets.

There were server issues until just a small time ago. Jobs that failed can be re-run now.

The Galaxy Support wiki has help for learning Galaxy. The top has learning links. Section 2 has more about histories, dataset status, and the like.

Best, Jen, Galaxy team

ADD REPLY • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

I've checked my saved histories and all of my data sets, still no results from the work flow. I've gona through my hand running each individual program for each dataset. Now I'm stuck waiting for cuffmerg to start running i've waited for a whole day and it still has started running and no error messages came up. I've decided to rerun the job and cancel the previous after it never started. I'm still waiting for this latest to start running and it's been over an hour now. I do not have any other programs running and I have plenty of disk space. Any additional help would be appreciated. I've already completed two other sets running cuffmerg and cuffdiff with no problem and I'm running through the same process with this one. I hope this information helps with solving my problems.

ADD REPLY • link written 2.5 years ago by sverga • 0

even my cuffmerge tool is waiting to run since 2 days. what could be the problem?

ADD REPLY • link written 2.5 years ago by brarp0619 • 10

2.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I suggest restarting the workflow, if you have not already and it is still missing under "Saved Histories". There may have been a transient problem with it starting up. I am not aware of any problems with this (and cannot reproduce it).

There was a bit of a backup for jobs earlier in the week. This is clearing up as the new Jetstream cluster is becoming fully configured. Jobs may queue for a longer time period right now than usual (and what we expect going forward). Allow queued jobs to run, without deleting and restarting, which only adds to delays in the vast majority of cases.

Workflows should launch immediately as a set of queued jobs - in the same history or a new one if you set up the run that way. If these jobs have not started yet (turned yellow) after two days, any that commented can send us an email from the same email address as your Galaxy account and we can take a closer look to be certain more is not going on. Send to galaxy-bugs@lists.galaxyproject.org and please include a link to this post so we can link the two.

I should have also provided more details with links in my initial comment. - https://wiki.galaxyproject.org/Support - https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k

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