These statements 
   $vec=${$$assignments{vector_files}}[$num_lib-1];
   $spli=${$$assignments{splice_files}}[$num_lib-1];

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Look like they could be a problem. If $assignments{vector_files} is a reference to an array it may not be working as you expect. Do $vec and $spli contain the values you expect ?

I usually code like this
   my $ref = $assignments{vector_files};
   $vec=$$ref[$num_lib-1];

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In reply to Re: why is my pm not finding the correct files by u671296
in thread why is my pm not finding the correct files by tangledupinperl

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