You said works for the first files, buy then die with the massage "Can not change sample_ACCTGG.fq to ACCTGG.fq". But when I print $new, it is "LA01.fq" that is correct.

but the code is  rename ($file, $new) or die "Can not change $file to $new, $!\n"; so the error message you quoted is incomplete, it doesn't state the reason it rename didn't work

This reason is everything

In reply to Re^3: change files names bug by Anonymous Monk
in thread change files names bug by Yuma248

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