ERROR: no unique fragment ends aligned

[MichySeq]

Hello,
for our 4C experiment we continually get the above error even though we are sure the experiment worked. Can you help debug why this would be? We do get a Frags object but then this at the end of the pipeline. We also replicate your demo perfectly. We were wondering if there was an optimium input sequence configuation, e.g. a min number of sequences or length etc ...... Below shows the output from the Fragment folder, all clues welcome.

        seqnames            ranges strand |     fe_id fe_strand    len129       pos        type
           <Rle>         <IRanges>  <Rle> | <integer> <numeric> <logical> <integer> <character>
    [1]     chr1             1-120      * |         1         5     FALSE         5   non_blind
    [2]     chr1         1030-1084      * |         2         3     FALSE      1080   non_blind
    [3]     chr1         1081-1221      * |         3         5     FALSE      1085   non_blind
    [4]     chr1         1421-1440      * |         4         3     FALSE      1436   non_blind
    [5]     chr1         1437-1741      * |         5         5     FALSE      1441   non_blind
    ...      ...               ...    ... .       ...       ...       ...       ...         ...

[5993726] chr25 37501227-37501236 * | 5993726 5 FALSE 37501231 non_blind
[5993727] chr25 37501387-37501393 * | 5993727 3 FALSE 37501389 non_blind
[5993728] chr25 37501390 * | 5993728 5 FALSE 37501394 non_blind
[5993729] chr25 37501876-37501882 * | 5993729 3 FALSE 37501878 non_blind
[5993730] chr25 37501879-37501973 * | 5993730 3 TRUE 37501969 non_blind

Best,
Michelle