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


Carrie,

    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
> > WICGR
> > [...]
>
> 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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