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.witham@jax.org The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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.witham@jax.org
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hello Iry, It seems that you need to update Cufflinks and include the helper script gtf_to_sam that comes with it. The current version supported by the wrappers available in galaxy-central and the latest galaxy-dist use version 1.3.0. Details, including links to download locations, can be found at: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies Please give this a try and let us know if you continue to have problems, Best, Jen Galaxy team On 10/19/12 12:22 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.witham@jax.org
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org
participants (3)
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Iry Witham -
Jennifer Jackson -
Jeremy Goecks