IUBio

Provision of DNA Sequencing as a core facility

Dr. Dr.
Fri May 30 08:28:50 EST 1997


>        At the moment, I am experiencing some bizarre problems, which I think
>relate to networking : In essence, the collection software is mixing up
>samples when new sample files are being generated after manual tracking
>of a gel. In addition, the gel file is jamming and during manual
>tracking etc. the mac is reporting a number of errors , such as
>Miscellaneous hardware errors, zero divide errors, chk errors and
>segment loading errors.
>
>        I am led to believe that these may stem from having file sharing open
>during collection of sequencing data. In response to these problems, I
>have wiped the hard disk, scanned for viruses, reloaded the software and
>even taken the precaution of having the logic board within the
>collection mac changed.
>
>        I would like some specific answers on the following questions :
>
>1. Should I shut down file sharing, period ,on the collection mac or
>just during collection itself ?

I can see no reason to keep file sharing off while you are not collecting.
I don't know whether my experience is relevant here because I'm using
a 373 with an ancient IIci for collection, but I have never turned file
sharing off (despite ABI's recommendations) even during collection, and
never had any problems.  Perhaps I get away with it because of the lower
rate of data transfer.

>2.As a follow on from the above, is it o.k to write sample files over
>the network form the collection mac,or is it preferable to have a second
>mac for disrtibuting data ?

My experience of networking on macs suggests that you frequently encounter
problems transferring large files.  It's much safer to write the initial
sample files to the collecting machine's hard disk, then transfer them
elsewhere later, once all the processing is done.  At least then if you
experience a glitch during file transfer you don't wreck the rest of
the analysis.

>3. I have started archiving data to an Iomega jaz drive, although I Am
>led to believe that these drives in the context of sequence analysis
>data may cause problems. Is there any truth in this ? Incidentally, when
>I first tried to install the driver software onto the collection mac it
>wouldn't have it and subsequently one of the apple talk extensions
>became jammed. Ever since then I have had problems like gel files
>jamming etc.

You may be experiencing an extension conflict between your driver and some
other extension.  Try using the extension manager to disable it while
collecting.  I use GeneJockeyII to convert my sample files to scf format
(which halves their size) before transferring them over the network to
an MO drive on another machine.  Basically, the fewer extensions you
have running on your collection machine the better.

>4. Has anyone experienced problems with writing gel files over the
>network ?

YES!  On my network, transferring a file of this size will inevitably
cause the transmitting machine to hang.  I've given up trying to fix
this.

Phil Taylor                         |        MRC Reproductive Biology Unit
                                    |        Centre for Reproductive 
Biology
                                    |        37 Chalmers Street
mbplt at seqnet.dl.ac.uk               |        Edinburgh EH3 9EW
ptaylor at hgmp.mrc.ac.uk              |        Scotland.




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