Processed 0 loci

[cooketho]

Please see if you can reproduce the following issue: When I ran the following command, I get the output shown below (bam file available at https://dl.dropboxusercontent.com/u/34969406/test.bam)

cufflinks -p 4 -o test_out test.bam You are using Cufflinks v2.2.2, which is the most recent release. [16:48:01] Inspecting reads and determining fragment length distribution.

Processed 1 loci. [_] 100% Map Properties: Normalized Map Mass: 151067.00 Raw Map Mass: 151067.00 Fragment Length Distribution: Empirical (learned) Estimated Mean: 241.42 Estimated Std Dev: 72.75 [16:48:02] Assembling transcripts and estimating abundances. Processed 0 loci. [_] 100%

When I ran the command using v2.2.1, either pre-built, or a version I built from source from here:https://github.com/smowton/cufflinks, I get the following output:

[16:48:38] Inspecting reads and determining fragment length distribution.

Processed 2 loci. [_] 100% Map Properties: Normalized Map Mass: 151371.54 Raw Map Mass: 151371.54 Fragment Length Distribution: Empirical (learned) Estimated Mean: 241.41 Estimated Std Dev: 72.75 [16:48:39] Assembling transcripts and estimating abundances. Processed 2 loci. [_] 100%

Is this simply due to differences in the default options, or is there a bug in v2.2.2? Thanks for your help and advice!