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thanks a lot smiling dragon

perl -e 'while (<>)
{
print;
$num = 2 if /fail_halt/i;
$num = 1 if (/failure/i && ($num < 1));
}
print $num
exit $num;'

-e is a command line option
for example on terminal you can say perl...

I thank u for taking interest in this problem.

The input file is like this, first whitespace is tab and subsequent are single spaces.
Here are 3 lines of the file.

PFA0165c ctg_6843
PFA0335w...

I use sed and awk. I am not a big expert but to some extent. I have file like this

PFA0165c ctg_6843
PFA0335w ctg_6843 ctg_6871 ctg_6977 ctg_6654 ctg_7052 ctg_6899 ctg_6840 ctg_7202...