Correct non-gzipped output from clustalo/align

[erikrikarddaniel]

PR checklist

Closes #XXX

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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In profile mode, Clustal Omega sometimes writes warning messages to standard out which ruins the output file as it's not recognizable fasta any more. I fixed this by writing the output with -o instead of >.

I didn't add any test as it requires quite a bit of new test data. I did test the updated module on my own test case however.