3700 thinks it is running but is idle. was Re: 3700 v 1.1

Mark Jung MARK.T.JUNG at USA.dupont.com
Wed Jul 12 15:14:15 EST 2000


    I was curious about this also.  We have talked about assaying data quality
in real time & shortening runs accordingly.  Can this be done?  We have
shortened the collection time to when phred quality drops below a certain
threshold, but this varies with each run.  Also have you tried playing with
event times in the run modules to shorten the processing times for plates?

Mark Jung
DuPont Nutrition & Health
Genomics Group
P.O. Box 6107
Newark, DE 19711
Mark.T.Jung at usa.dupont.com

Phillip San Miguel wrote:

> Carrie Sougnez wrote:
> > [...]  PE thinks
> > they have a fix for the intermittant, pausing out during sample transfer
> > error (usually run #2).   They sent us an EXE file that shuts off the
> > diagnostics port on the instrument (which they belive is causing the
> > instrument to pause out).  We have not yet confirmed that this is a
> > "solid fix" though.
> >
> > Carrie Sougnez
> > Coordinator, Sequence Detection Group
> > [...]
> Carrie,
>     I got the impression (perhaps false) that at Whitehead you have some
> method of assaying the quality of reads coming off your machines during a
> run. Further that you stop runs that are no longer producing good data so
> that the next run can begin earlier. Is this the case?
>     I'm asking because I may have gotten the error you speak of above. What
> happened was that the 3700 was "running", the camera shutter was clicking (I
> think that is what makes the clicking sound during data collection...) but
> no data was being displayed to the array view of the screen. Further, no
> data seemed to be stored to the database.
>     If I hadn't been sitting next to the 3700, I wouldn't have noticed what
> was going on. It just looks like a run that produces no data and no errors.
> I have always attributed this to my stopping some runs earlier in the batch
> (or maybe it was the previous batch)[1]. Any chance that is what is
> happening at Whitehead?
> Phillip San Miguel
> Purdue University Genomics Core Facility
> [1] See
> http://bionet.hgmp.mrc.ac.uk/hypermail/autoseq/autoseq.200002/0013.html
> where I give more details. Also
> http://bionet.hgmp.mrc.ac.uk/hypermail/autoseq/autoseq.200003/0007.html
> where I agonize further on this topic.
>     Also Bruce Roe mentions a phenomenon that sounds similar: "Fortuantely,
> 'knock on wood', all 5 have been up and running all week except for one that
> ran and didn't seem to see or collect any signal (even though re-running the
> same plate gave beautiful signal on the same instrument after restarting
> both the 3700 and the associated computer)" see
> http://bionet.hgmp.mrc.ac.uk/hypermail/autoseq/autoseq.200003/0006.html
> ---


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