come inserire una nuova riga se una riga ha più di 60 caratteri

Prova:

$ awk '{print $1; for (i=1;i<=length($2);i=i+60) print substr($2,i,60)}' file
>Directory1/file3
CTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTTTCCCCCCCCSCBCC
CCCCCCSCTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTTTCCCCCC
CCSCBCCCCCCCCSCTTSCCCTTTTTSEEEEECGGGSCEEEEECCCSSBCCCSCCCCCTT
TCCCCCCCCSCBCCCCCCCCS
>Directory1/file4
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAA

Come funziona:

1. print $1

   Questo stampa il primo campo sulla riga.

2. for (i=1;i<=length($2);i=i+60) print substr($2,i,60)

   Per il secondo campo sulla riga, stampiamo 60 caratteri alla volta finché non raggiungiamo la fine del campo.

Puoi usare GNU coreutils fold :

fold -w60 file