I'm running Cufflinks (2.2.1) on a set of RNA-seq alignments that I did with STAR. I'm using these options:

/home/user1/Data/Softwares/cufflinks-2.2.1/cufflinks -p 6 -u -o ./Cufflinks/ERR036348_pass-2 ./Alignments/ERR036348_pass-2/ERR036348_pass-2_Aligned.sortedByCoord.out.bam

In every instance I get the message: "WARNING: Multi-Hit not found". I pasted the beggining of the output of a run I did.

[00:12:17] Inspecting reads and determining fragment length distribution.
> Processed 51509 loci.                        [*************************] 100%
> Map Properties:
>       Normalized Map Mass: 28150478.05
>       Raw Map Mass: 28150478.05
>       Number of Multi-Reads: 2479202 (with 6180369 total hits)
>       Fragment Length Distribution: Empirical (learned)
>                     Estimated Mean: 353.78
>                  Estimated Std Dev: 35.57
[01:36:09] Assembling transcripts and initializing abundances for multi-read correction.
> Processing Locus 1:86701401-87057627         [                         ]   2%
WARNING: Multi-Hit not found (86357258,86357334).

WARNING: Multi-Hit not found (86357265,86357341).

WARNING: Multi-Hit not found (86357276,86357352).

In this particular library, I got the warning 1997 times.

What is happening? Should I add a option to Cufflinks?