Given two fasta files, attempting alignment:
==> seq1.fasta <==
>seq1
DVARNTGAYTS
==> seq2.fasta <==
>seq2
EVACNTGAYTS
Both needle and stretcher crash:
$/usr/local/bin/needle seq1.fasta seq2.fasta needle.out
Needleman-Wunsch global alignment of two sequences
Error: Sequence is not nucleic
Error: Unable to read sequence 'seq2.fasta'
Died: needle terminated: Bad value for '-bsequence' and no prompt
Error happens even when specifying
/usr/local/bin/needle seq1.fasta seq2.fasta needle.out -datafile EBLOSUM62 -auto Y -awidth3 999999999
Can narrow it down to this confusing example:
THIS WORKS
==> seq1.fasta <==
>seq1
SVAS
==> seq2.fasta <==
>seq2
SATA
THIS CRASHES NEEDLE
==> seq1.fasta <==
>seq1
SVAS
==> seq2.fasta <==
>seq2
SLTA
I can't find any reason why.
I got the same error (
EMBOSS 6.3.1
). What's interesting is that needle works fine when you change the order of your input sequences (providingseq2.fasta
as the first one and thenseq1.fasta
).... I thought this was a weird error, the order mattering makes it twice as much.