Thanks for your reply! Well, it's only the  my $prot3 = $seq->translate(2); part that does not work, which makes me think the input is fine since it works for the $prot and $prot2.

However, here is sample input if it helps! The file contains 194,503 of these sequences, but here are a couple for an idea:

>3HSAA000001 CA000001
tgcagccgcgggcccagggtgctgttggtgtcctcagaagtgccggggattctggactgg
ctccctcccctcctgttgcagcacaaggccggggtctctggggggctggagaagcctccc
tcattcctcccaggaattaataaatgtgaagagaggctctgtttaaaatgtctttggact
cccagggctgagtgggctgggatctcgtgtcctcaa
>3HSAA000002 CA000002
tgcagccgcgggcccagggtgctgttggtgtcctcagaagtgccggggattctggactgg
ctccctcccctcctgttgcagcacaaggccggggtctctggggggctggagaagcctccc
tcattcctcccaggaattaataaatgtgaagagaggctctgtttaaaatgtctttggact
cccagggctgagtgggctgggatctcgtgtcctcaaagtggatgggttctggggtggctc
ctgaggtagaggagtggagaactggctcttaagagcacagttttcttttcttttttcttt
tttgagacagggtctcacactgtcacccaggctggagtgcagtgttgcagtccggctcac
tgcagttttgacctcccaggctcaagcgatcctcctgcctcagcctcccaagtagctggg
agcctgggcatgcatcgccacgtctggctaattattattttttgtagacagggtctcact
gtgttgcccaagcttgtcttgaactcctggccttaagtgatcctcccacctcagcctcct
gagtagctgggactacaggcatgagccaccatgcctggccaactcacatttttctttcta
ttatttattttttgtagagatgagtctcactatgttgcccaggctggtcttgaactcttg
ggctcaagtgatcctcccgcctcagcctcccaaagtgttgggattacaggtgtgagccac
agcacctggccaaccaacacttctcagggcctctttcatctgtgctcttccaggatgctg
cctcttactccctgggcacctcggcctggtcccagcaggtatgggcagttgcttgaggct
ccagacatactcacctctacctcgaccacatcaaccccatcaccaagaggaggttcaggg
aagctgcattttgtggtcttgtcctcccagtccagggtggtagtgctgggctgttcccag
cctcccacagcagagctggacgctgtggaaatggctggattcctctgtgttctttcccat
tatccctcagctctgagtcctcttgtgccatctgacatctgatgccttcccaaccactgc
cgagtttctgcctggagcagggcctcaaggccctggcacacagaagatgcgtatcagtat
tatcaaccaatagttgatgaattgtgtttttcaacgaatttgctagtgatctggtttact
gccttagtaatatctagttcctaatatgcctatgccttttaatgtctgcacagtctatga
tgatgtcacttctctcaagcctgatgtgtcctctctctctttcttgctagtggtttatca
atttttaaaaccttttcttgtttatttgtttttgagacagaattttgctcttgttgccca
ggctggagtgcaatggcgtgatcttggctcacagcaacctctacctcctgggttcaagtg
attctcgtgcctcagcctcctgagtagctgggctgacaggcacccaccaccacacccagc
taatttttatgtttttagtagagatggggtttcaccttgttgggtggccaggctggtctc
caactcctgagctcaagtgatccacccgcctcagcctcccaaagtgctgggattacaggg
gtgagccaccacgcccagccccagcttagttttttaaaaagtttattttagccattctaa
taggtatgtagacatatctaatagtggttttccttgcgtttccttaatgtctgatgatgt
taagcattttttccccaagtgcttagttgccatctatatagcatctttgatgaaatgtct
gtttatatattttgcacactttaaaatattgggttgttttcttt
>3HSAA000003 CA000003
tgcagccgcgggcccagggtgctgttggtgtcctcagaagtgccggggattctggactgg
ctccctcccctcctgttgcagcacaaggccggggtctctggggggctggagaagcctccc
tcattcctcccaggaattaataaatgtgaagagaggctctgtttaaaatgtc

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In reply to Re^2: Error with Bio::Seq Translate by dmbNEWB
in thread Error with Bio::Seq Translate by dmbNEWB

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