3700 thinks it is running but is idle. was Re: 3700 v 1.1 Data extractor/Change Poly Wizard Conflict?

Phillip San Miguel pmiguel at purdue.edu
Mon Mar 20 12:51:32 EST 2000

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
> [...]

    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
where I give more details. Also
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


More information about the Autoseq mailing list

Send comments to us at biosci-help [At] net.bio.net