I bet your log data is actually in there when sending via UDP directly from your Netapps, however, I imagine it is your host field of the Netapp that is skewed.
Have a look at the logs first that you are writing to disk from it via the syslog to a file, I'm guessing if they are like mine they look like:
date time hostname [hostname: process:priority]: message
That first 'hostname' is getting written by the intermediary syslog server you are sending logs to first, which when you have splunk read this file picks up the host filed properly.
What I would do to see if the direct from Netapp logs are in splunk is to instead of putting in your search:
host=mynetappname
which I am guessing you are doing, do instead:
host=*mynetappname*
I'm betting it is the host field at index time that is getting munged when you are sending direct. Netapp for whatever reason jumbles the hostname in with the process and syslog priority and I bet that is causing issues here - at least from my experience with their logs.
Hope this helps,
Scott
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