Every time you use the input operator (<>), you read a new line. You can read it into a variable, but you're not doing that, so it goes directly into the special variable $_. You read a line in the while condition, and then clobber it by reading the next line from the file in the split operation.

Do this instead:

while (my $line = <>) {
    @chunks = split(/","/, $line);
# other stuff
}
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Or use Text::CSV to split up your comma separated values, if your data has complicated stuff like commas within your quotes.