Error: number of labels must match number of conditions

[shpyang]

Hi Guys,

I am trying to repeat the Nature protocol paper, however, I have a little bit trouble with the cuffdiff step. Followings are the scripts and the error messages. Any comments will be appreciated!

cuffdiff -o ./diff2 -b ~/pak/ensembl/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/WholeGenomeFasta/genome.fa -p 20 -L C1,C2 -u ./merged_asm/merged.gtf ./C1_R1/hits.bam, ./C1_R2/hits.bam, ./C1_R3/hits.bam ./C2_R1/hits.bam, ./C2_R2/hits.bam, ./C2_R3/hits.bam

cuffdiff: /lib64/libz.so.1: no version information available (required by cuffdiff)
You are using Cufflinks v2.1.1, which is the most recent release.
Error: number of labels must match number of conditions

[dpryan]

Remove the spaces following the commas:

./C1_R1/hits.bam,./C1_R2/hits.bam,./C1_R3/hits.bam ./C2_R1/hits.bam,./C2_R2/hits.bam,./C2_R3/hits.bam

[shpyang]

It works!

Thank you very much!