I generated SAM files using GSNAP. Sorted them using the following command:

sort -k 3,3 -k 4,4n identifier.unpaired_uniq > file

Now, I'm able to run cufflinks but when I run cuffdiff, it says:

[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[17:10:05] Loading reference annotation.
[17:10:08] Inspecting maps and determining fragment length distributions.)

And then keeps running. It's been days but it is still running. Here is the cuffdiff command:

cuffdiff merged_asm/merged.gtf P1_02.uniq.sorted,P2_02.uniq.sorted Control_P1_12.uniq.sorted,Control_P2_12.uniq.sorted,Control_P1_13.uniq.sorted,Control_P2_13.uniq.sorted -o diff_out.P_02vsContol -p 8 -L P,Control

Can someone point out where I'm going wrong?

Thanks