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use strict;
use warnings;
...
        }
    }
}

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,CLS_S3_Contig100,1,,,0
,CLS_S3_Contig100,2,,,0
...
CLSS3627.b1_F19.ab1,CLS_S3_Contig10031,62,11,0.5129,1
,CLS_S3_Contig10031,63,,,0
CLSS3627.b1_F19.ab1,CLS_S3_Contig10031,64,11,0.5789,1