Question: Galaxy job taking bit too long for uploading and processing datasets
gravatar for j.zhang-41
2.5 years ago by
j.zhang-4110 wrote:

I am trying to upload several ChIP-seq sequencing results from my own computer through ftp. Most of the files were successfully uploaded, but some were not and still queuing to be processed. Meanwhile I tried to change the datatype of uploaded files from fastq to fastqsanger format, which usually took a few minutes, but this time it took more than 12 hours and still running (with yellow background). I only used half of my space allowance, so I was just wondering if there is any trouble with Galaxy server and if there is anyway to resolve this quickly. Thank you very much!!

galaxy chip-seq • 972 views
ADD COMMENTlink modified 2.5 years ago by carlfeberhard390 • written 2.5 years ago by j.zhang-4110

Hello, j.zhang-41: If you use the refresh the page, do the history datasets change state? Have they run? Or do they remain in the running state regardless of the page refresh?

ADD REPLYlink written 2.5 years ago by carlfeberhard390

Hello, carlfeberhard: Thank you for your reply! I have tried to refresh both the Galaxy webpage and the history several times and the datasets state does not change. The ones that are running (Yellow background) is still running, but it already took more than 10 hours. Consequently, all the rest datasets and operations could not be queued for processing. I simply changed the data format from fastq to fastqsanger format. I have done it before, it usually took less than 5 minutes. It just seemed like somehow the history got stuck...

ADD REPLYlink written 2.5 years ago by j.zhang-4110
gravatar for carlfeberhard
2.5 years ago by
United States
carlfeberhard390 wrote:

Thanks for the information, j.zhang-41. This may be due to load on the main Galaxy site then. When the data type of a dataset is changed, metadata for the file is recomputed. This often is done through one of the cluster job queues.

Currently the mainGalaxy cluster is working through a significant amount of jobs that had backed up over the last several days while new work was incorporated into the cluster. Our hope is that, when the cluster is fully and properly configured, jobs will be much quicker.

We really appreciate your patience.

ADD COMMENTlink written 2.5 years ago by carlfeberhard390

Thank you very much for your help, carlfeberhard! The problem has been resolved and the history is now running smoothly! Thank you!

ADD REPLYlink written 2.5 years ago by j.zhang-4110
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