Cuffdiff error???

[Sciurus]

Hi everybody,

I keep getting the same error when trying to run cuffdiff:
number of labels must match number of conditions.

I have two groups/ treatments with 4 replicates each.

Now, I've read numerous other posts with suggestions like leaving out spaces between commas, etc. but nothing works.

Please help!

I'm using Cufflinks-2.2.1 on Linux.

My Code is:

cuffdiff -p 12 -o ./cuffdiff/ -b /path/to/genome.fa –library-norm-method quartile -L TreatmentA,TreatmentB ./merged/merged/merged.gtf \
./cuffquant/Ctrl_1_abundances.cxb,./cuffquant/Ctrl_5_abundances.cxb,./cuffquant/Ctrl_9_abundances.cxb,./cuffquant/Ctrl_13_abundances.cxb \
./cuffquant/Sample_2_abundances.cxb,./cuffquant/Sample_6_abundances.cxb,./cuffquant/Sample_10_abundances.cxb,./cuffquant/Sample_14_abundances.cxb

Thanks!!!

[GenoMax]

Have you tried to run with "-v" (verbose) option to see if you get any additional diagnostic output?

[Sciurus]

Thanks for the suggestion!

Strangely enough, I retyped the whole command and now it runs even though everything is still the same.

Maybe there was some weird formation thing going on in my editor?

[GenoMax]

Always use a programmer's editor if you are editing the command line on a PC (Notepad++)/Mac(Textwrangler).

[Sciurus]

Yes, I am using Notepad++ but I have no other explanation for what went wrong before...