Command line:
/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/cufflinks --no-effective-length-correction -g /data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf -L SCAN-untr-0h-a --no-update-check --library-type fr-secondstrand --num-threads 1 -q -o SCAN-untr-0h-a/accepted_hits_ensembl_novel bams/SCAN-untr-0h-a.bam2 
[20:31:36] Loading reference annotation.
[20:32:02] Inspecting reads and determining fragment length distribution.
Processed 258886 loci.                      
> Map Properties:
>	Normalized Map Mass: 34029226.14
>	Raw Map Mass: 34029226.14
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
[20:40:35] Assembling transcripts and estimating abundances.
Processed 258886 loci.