May just be a typo but on line 6, "- file" should be "-file".

From the first error message, I'd guess that this was an input format error. Little things like spaces in the fasta ID could kill the parser. Check your input around line 81643. If this script works on a small portion of the input, try with a region around the error.

The second error message could just be an artifact because it really should know where "blastall" is kept. Just to make sure, check $blast->executable('blastall').

In reply to Re^3: Aligning sequence by igelkott
in thread Aligning sequence by Anonymous Monk

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