As a WebTrends user too, might I suggest looking at the Preprocessing and
PostProcessing capabilities of WebTrends.  I was able to write a tiny
little .bat file that will run at the start of the analysis.  This .bat
file takes care of the needed FTP to bring over the .log files from the
iSeries.  Another one at the end removes them.

Let me know if an example is needed.

-Jeremy


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