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missing base calls

Marvin.Stodolsky Marvin.Stodolsky at mailgw.er.doe.gov
Thu Mar 21 14:06:22 EST 1996


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From: lsimon at rsvs.ulaval.ca_at_internet at X400PO
Date: 3/20/96 10:46AM
To: Marvin Stodolsky at ER-GTN
*To: nobody at net.bio.net_at_internet at X400PO
Subject: missing base calls
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Perhaps a way to implement an automatic check for Occurrences in this 
class is to have a clock output in parallel with raw trace data.
A break in the continuity of the clock record could then Signal a
gap in receipt of trace data at the data repository.

MS

______________________________ Forward Header 
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Subject: missing base calls
Author:  lsimon at rsvs.ulaval.ca_at_internet at X400PO
Date:    3/20/96 10:46 AM


We have got an unusual occurrence last week on a 373 Stretch sequencer. All 
36 analyses were missing about 20 bases at about position 300 in their 
sequences. There were almost no indication that anything went wrong with 
that run, and it took us a while to detect the problem, essentially by 
finding a gap when comparing data with known sequences.
     
We now think that this problem occurred when an automatic backup somehow 
interfered with the collection of data. Has anybody ever seen that? We use 
Retrospect 3.0 to backup all our machine over an ethernet network, but will 
be extra cautious not to allow it to connect to the one collecting data 
from the sequencer when its operating.
     
What surprised me the most was that the traces and base calls contained 
absolutely no clue that anything had gone wrong, and the problem might very 
well go unnoticed if the sequences cannot be independantly doublechecked.
     
BEWARE OF ANY PROGRAM OR NETWORK ACCESS TO THE COLLECTING COMPUTER!!!!
     
Sequencingly yours,
     
     
Luc Simon
     
Coordonnateur des services scientifiques
1125 Charles-Eugene Marchand                         tel.  (418) 656-5496 
Universite Laval                                              fax.  (418) 
656-7176
Sainte-Foy, Que G1K 7P4




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