DNAseq: 3700 crash due to comments text

Phillip San Miguel pmiguel at purdue.edu
Fri May 25 11:13:13 EST 2001

Bernd Weisshaar wrote:

> Dear DNAseq'ers,
> since some time we have the problem that our 3700 crashes during data extra=
> ction. All data (as far as we know) from the run in question are lost, and =
> a complete database purge is required to get the instrument back to work. I=
> nitially, we thought that the crashes were unpredictable (as did the Abi se=
> rvice).
> Now, we have traced the problem down to our comment text in the "Comment" c=
> olumn of the plt file. We use this field to transfer information from our L=
> IMS to the sequence trace (!) file for subsequent automatic analysis of the=
>  data, and the length did increase over time when more information was tran=
> sferred in an easy-parsable (and human-readable) way. An example of an info=
> rmative plt file is shown here:
> http://adis.mpiz-koeln.mpg.de/Adis/Example-Gels/3700-DataExtr-comments.html
> [...]

    From what you show it looks like there is a 128 (2^7) byte limit on the
comment field that Data Collection doesn't check. I have noticed a 32 (2^5) byte
limit on the sample name, but Data Collection will refuse to import a plate
record that has sample names over 32 bytes. (And it even generates an obscure
error message to help you find the problem.) Data Collection apparently doesn't
check the field length for comments and the database ends up corrupted. Nasty

Phillip San Miguel
Purdue Genomics Core Facilty


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