Off topic:Cuffldiff is hanging at "99% complete"

Question

[M K]

I am running cuffdiff but it is hanging at "99% complete", my commad as follows:

cuffdiff  -o /disk1//Diff_mouse  -b  /disk1/Mouse_genome/Bowtie2Index/genome.fa  -p 14  -L Brain,Heart,Kidney  -u Mouse_assemblies/merged.gtf   ./Mouse_brain/accepted_hits.bam,  ./Mouse_heart/accepted_hits.bam,  ./Alignment/Mouse_kidney/accepted_hits.bam

Map Properties:
      Normalized Map Mass: 72227841.38
      Raw Map Mass: 68981175.37
      Number of Multi-Reads: 11729580 (with 38235552 total hits)
      Fragment Length Distribution: Truncated Gaussian (default)
                    Default Mean: 200
                 Default Std Dev: 80

[22:58:05] Calculating preliminary abundance estimates

Processing Locus X:149357995-149358303       [************************ 99% ab@clyi:/disk1/Diff_mouse>

Then I tried to use the option -M/--mask-file <mask.(gtf/gff)> as follows:

cuffdiff  -o /disk1//Diff_mouse  -b  /disk1/Mouse_genome/Bowtie2Index/genome.fa -p 14 -L Brain,Heart,Kidney -M Mouse_assemblies/merged.gtf ./Mouse_brain/accepted_hits.bam, ./Mouse_heart/accepted_hits.bam, ./Alignment/Mouse_kidney/accepted_hits.bam

but it gave me the following error

Cuffdiff Requires At Least 2 Sam Files

Please help