cuffdiff error: number of labels must match number of conditions

[Giuseppe1995]

Hi!
I am trying to run cuffdiff on a previously merged gtf file i created with cuffmerge. The command I'm running is the following:

cuffdiff ./diff_exp -p 15 -b /srv/ngs/analysis/dalteriog/reference_genomes/hs/GRCh37.fa -u --library-type fr-secondstrand -L EMATO,GR2108,GR2108m,GR2108p merged_assemblies/merged.gtf EMATO-15/02.EMATO-15.bam,EMATO-26/02.EMATO-26.bam,EMATO-27/02.EMATO-27.bam,EMATO-28/02.EMATO-28.bam,EMATO-58/02.EMATO-58.bam,EMATO-64/02.EMATO-64.bam GR2108-1/02.GR2108-1.bam,GR2108-2/02.GR2108-2.bam,GR2108-3/02.GR2108-3.bam GR2108m-1/02.GR2108m-1.bam,GR2108m-2/02.GR2108m-2.bam,GR2108m-3/02.GR2108m-3.bam GR2108p-1/02.GR2108p-1.bam,GR2108p-2/02.GR2108p-2.bam,GR2108p-3/02.GR2108p-3.bam

and I'm getting the following error message:

Error: number of labels must match number of conditions

Now, I have looked up the web, and every blog stated that the problem was a mismatch between the number of labels (defined by -L) and the bam files per condition, which have to be comma-separated if intra-condition and space separated if inter-condition. I wrote the code exactly as that as you can see above: there are 4 labels (EMATO,GR2108,GR2108m,GR2108p) and four groups of bam, one for condition, in their respective directory.

I've been puzzling for one day to find out which is the problem, and I fear that may be something stupid that I did not notice, although I analyzed my code extensively.

Another Hypothesis I've made is that the first group consists of 6 files, while the other of 3, and this may be a problem somehow.

Thank you in advance,
Giuseppe