Ignore header when performing awk command - not working

Question

I know several questions have been asked about ignoring the header using the awk command, but I have tried a bunch of the suggested methods and it still isn't working for me.

I am using awk to cut characters from a string, but the output file is being generated without the header, even though the header doesn't contain the characters that I am trying to cut.

Here is my command:

cat input | awk -F '|' '{print$2}' > output

This command does what I need, but my header rows are left empty. I am trying to print everything after the "|" symbol, but I want to keep the headers in my input file (which involves the first two rows). I have tried using NR>2, but to no avail. Maybe I am not placing the ignore header command in the right place. Any help is greatly appreciated. Thank you!!

Here is a sample of the input:

Total Number of Mapped Reads = XXXX
Genome Final Guess Final Hit 
ACCN2|Bacterial Species 5.4 3.5
ACCN4|Bacterial Species 2.6 8.7

Desired Output:

Total Number of Mapped Reads = XXXX
Genome Final Guess Final Hit 
Bacterial Species 5.4 3.5
Bacterial Species 2.6 8.7

Answer 1

Your sample command prints the second field of | separated file. SInce the first 2 records only have 1 field, nothing gets printed with $2, instead print the last field $NF:

$ awk -F\| '{print $NF}' file
Total Number of Mapped Reads = XXXX
Genome Final Guess Final Hit 
Bacterial Species 5.4 3.5
Bacterial Species 2.6 8.7

Answer 2

You can use tail to skip a specific number of header lines here is an example:

command | awk  '{print $1}' | tail +2

this will skip the first 2 lines after performing awk on the first field of the command result.