> It looks like the output only occurs when cufflinks can't run on the
> provided dataset.  I checked my inputs, and I think that is the
> problem...its a sam file from bowtie, not from tophat, hence not a sorted
> sam file.  Perhaps this stderr message doesn't matter after all, its just
> misleading...
Yes,  I think you are correct. Let us know if you have more questions.

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