What is the average queue time for Bowtie2?

Question: What is the average queue time for Bowtie2?

21 months ago by

United States

Hi all, I have started a bowtie2 alignment (RNAseq, 100 bp paired end, two 15GB FASTQ files against hg19) yesterday, about 20 hrs ago, and the job is still waiting to start (grey boxes). I am wondering if this is normal, since previously, bowtie2 alignments for me usually started within a few minutes after the source files had become available. Should I just wait longer, or would you suggest I should cancel the current jobs and restart them? I noticed when I started the job yesterday I had some difficulties with galaxy, as connection to the server was unstable and the sites would time out frequently. Could this have caused some problems with job submission? Thanks for your help! Christian

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modified 21 months ago • written 21 months ago by pfaller.christian • 0

21 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If working at http://usegalaxy.org, then I can let you know that there were a few problems yesterday, now resolved. Also, the server is being restarted right now and that will "look" like a problem for a minute or so.

Allow jobs to stay queued. Queue times can vary, but if the server is busy (as it is now) certain jobs may queue for 24 hrs or a bit longer. Please see: https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

Thanks, Jen, Galaxy team

ADD COMMENT • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k

21 months ago by

pfaller.christian • 0

United States

pfaller.christian • 0 wrote:

Thank you so much for your explanation, Jen! Really appreciate it!

ADD COMMENT • link written 21 months ago by pfaller.christian • 0

Update: The server had more changes today, so if you still have job delays or unexplained errors, try a re-run now. Jobs are queuing much quicker (right now - this might change depending on server load throughout the day/weekend).

ADD REPLY • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks, Jen! I re-started the job and this time it started running after just a few moments. It really must have been the server updates or bad timing (job submission during an update) that held my jobs in queue.

ADD REPLY • link written 21 months ago by pfaller.christian • 0

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