Hi, We have two Filter FASTQ jobs running on the Galaxy public server. Both jobs have been running for more than four days. This seems like an excessive amount of runtime. Do Filter FASTQ jobs normally take this long to run? ---------------------------- Richard
On Thu, May 9, 2013 at 12:27 PM, Casey,Richard <Richard.Casey@colostate.edu> wrote:
Hi,
We have two Filter FASTQ jobs running on the Galaxy public server. Both jobs have been running for more than four days. This seems like an excessive amount of runtime. Do Filter FASTQ jobs normally take this long to run?
Which FASTQ filtering tool exactly are you referring too? The one called "Filter FASTQ reads by quality score and length" in the left hand column, tool ID fastq_filter? How big were the input files? Peter
Yes, it's the "Filter FASTQ reads by quality score and length" in left-hand pane. There were actually four separate runs on four datasets. Two of them finished in about a day but the other two have been running for about 4 days. The input files range in size from 6GB - 11GB Today, the two 4-day jobs both aborted with error message: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. ------------------------------------------- Richard
-----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: Thursday, May 09, 2013 7:46 AM To: Casey,Richard Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] Filter Fastq
On Thu, May 9, 2013 at 12:27 PM, Casey,Richard <Richard.Casey@colostate.edu> wrote:
Hi,
We have two Filter FASTQ jobs running on the Galaxy public server. Both jobs have been running for more than four days. This seems like an excessive amount of runtime. Do Filter FASTQ jobs normally take this long to run?
Which FASTQ filtering tool exactly are you referring too? The one called "Filter FASTQ reads by quality score and length" in the left hand column, tool ID fastq_filter?
How big were the input files?
Peter
Hi Richard, The public Main Galaxy server has been very busy lately. To let you know, the size of the job will not determine when a job will start, only the time it was started/queued with respect to other user's jobs also queued and in less common circumstances the specific type of job (that requires a particular cluster node type - this was not the case for your job). How long a job executes (will be in the "yellow" running state) is related to the size of the inputs, the type of job, and parameters. I see that these have now failed with a cluster error - please re-run the failed jobs one more time. If you continue to have problems, please submit one of the error datasets as a bug report, leaving all inputs/outputs undeleted. http://wiki.galaxyproject.org/Support#Reporting_tool_errors Very sorry that this was causing confusion. And thanks Peter for the help! Jen Galaxy team On 5/9/13 4:27 AM, Casey,Richard wrote:
Hi,
We have two Filter FASTQ jobs running on the Galaxy public server. Both jobs have been running for more than four days. This seems like an excessive amount of runtime. Do Filter FASTQ jobs normally take this long to run?
---------------------------- Richard
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participants (3)
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Casey,Richard -
Jennifer Jackson -
Peter Cock