When we ingest logfiles which contain Java we configure the linebreaker manually. This means that the whole java dump will be in one event instead of mixed up by the splunk auto parsing.
In those cases our props.conf looks like this:
[yoursourcetype]
LINE_BREAKER = ([\r\n]+)\d{4}-\d{2}-\d{2}\s\d{2}:\d{2}:\d{2}
SHOULD_LINEMERGE = false
TRUNCATE = 100000
MAX_TIMESTAMP_LOOKAHEAD = 30
NO_BINARY_CHECK = true
TIME_FORMAT=%F %T
TIME_PREFIX=^
LINE_BREAKER should contain the timestamp after the ([\r\n]+) and you probably want to increase TRUNCATE to at least 100000
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