I am trying to run Cuffcompare on a set of 6 Cufflinks-generated datasets
(3 replicates of 2 conditions).  I am consistently getting the following

Error running cuffcompare. Warning: Your version of Cufflinks is not
up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to
benefit from the most recent features and bug fixes
Error: no XLocus created for transcript CUFF.34072.1 (file ./input3)
[2, 2], on chrY+:274296-277218

However, if I run Cuffcompare on the 2 conditions separately (3x Cufflinks
datasets), everything works fine.
Does anyone know why this is?


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