Hi Folks,

I have run into an issue with cuffmerge.  I am attempting to run it with mm10 
references and it fails attempting to execute gtf_to_sam.  The following is the 
actual error message I get:

Error running cuffmerge.
[Fri Oct 19 15:13:55 2012] Beginning transcriptome assembly merge

[Fri Oct 19 15:13:55 2012] Preparing output location cm_output/
[Fri Oct 19 15:14:15 2012] Converting GTF files to SAM
gtf_to_sam: invalid option -- F
cufflinks v0.9.1
Usage:   cufflinks [options] <transcripts.gtf> <out.sam

-r/--reference-seq                        reference fasta file for sequence 
bias correction     [ default:   NULL ]
Error: could not execute gtf_to_sam

I have assured that the indexes and loc files are correct and in place.  Can 
someone point me in the right direction?


Iry Witham

Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609
Phone: 207-288-6744
email: iry.wit...@jax.org

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