The first header in $line reads through the whole file and then for the second and subsequent headers the filehandle FH will return eof.   You need to either open $fn inside the foreach loop or use seek to return the filehandle to the beginning of the file inside the foreach loop.

In reply to Re: While loop printing only one fasta file by jwkrahn
in thread While loop printing only one fasta header file by ashnator

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