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