Is that all your code? Currently it has only 33 lines, so I am a bit puzzled.

Update:
The Problem is this line:

print $query->('dssp file used is $dssp_file');
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You must replace it with a simple print

print "dssp file used is $dssp_file";
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Note the use of double quotes here. With single quotes your variable will not be interpolated.

Or use one of the modules output methods.

print $query->h1("dssp file used is $dssp_file");
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