Cufflinks then Cuffdiff

[plefebvre]

Hi there
I have ran a RNA-seq on Illumina GII, and processed the bam files on the Galaxy server. Everything ran smoothly untill I tried to run Cuffdiff on may assembled transcript files which always yields an error as this

566: Cuffdiff on data 492, data 493, and data 521: CDS diff
An error occurred running this job: cuffdiff v0.9.3 (1649)
cuffdiff -q -p 8 -Q 0 -c 1000 --FDR 0.050000 -N -r /galaxy/data/mm9/sam_index/mm9.fa /galaxy/main_database/files/002/338/dataset_2338625.dat /galaxy/main_database/files/002/337/dataset_2337232.dat /galaxy/main_database/files/002/337

Has somebody ever ran into this kind of problem (the Glaxy team sais this is a Cufflinks problem, but no answers yet from those guys ...)
Thanks

[honey]

error in Cuffdiff

It appear that you are running on Galaxy you may like to post your question on their mailing list and may be there is some glitch in Galaxy