Try upgrading your Cufflinks binaries and see if that solves the problem; the 
wrappers are designed to support versions 1.3+, but I'm not sure if they'll 
work with older versions.

Best,
J.

On Oct 19, 2012, at 3:22 PM, Iry Witham wrote:

> 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
> Options:
> 
> -r/--reference-seq                      reference fasta file for sequence 
> bias correction     [ default:   NULL ]
>       [FAILED]
> 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?
> Thanks,
> 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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