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uniq needs sorted input. man uniq:Unfortunately, your sample has only unique second fields so it can't be tested against. Adding a few non-unique lines, this may lead to the desired result:sort -k2...

How about trying sth on your own?

Nevertheless, try awk 'FNR==NR {if (/^>/) P=$0; else T[$0]=P; next} $0 in T {print T[$0]; print}' file2 file1
>ERR315352.12390252_5250 5250...

Not sure I understand your request, and having two sample files that don't match doesn't help either.

Anyhow, tryawk 'FNR==NR {C[$2]=$1;next}
FNR==1 {print "Count Read...