cuffmerge error

[wangli]

Hi, I am confronted with some errors when doing cuffmerge analysis.

/home/bin/cuffmerge -g Ptrichocarpa_156_gene.gff3 -s Ptrichocarpa_156_hardmasked.fa -p 10 assemblies.txt

[Wed May 30 09:48:20 2012] Converting GTF files to SAM
[FAILED]
Error: gtf_to_sam not found on this system. Did you forget to include it in your PATH?

I checked very carefully with my directory /home/bin and found that gtf_to_sam is actually in this directory. I cannot understand why the software cannot find it.

Sorry for my naive questions.

Any comments are very appreciated.

[kriskris]

I have the same problem! Did you ever find a fix?

[wangli]

Hi, gtf_to_sam should be specified in your PATH.
You need to type the following command in your terminal:
PATH=$PATH:/PATH/TO/gtf_to_sam

[kriskris]

Thanks wangli, but that doesn't appear to be the problem. Any other ideas?

[wangli]

you can look into the following thread:

http://seqanswers.com/forums/showthread.php?t=15092

[zhwang]

I was running cuffmerge and got the following message. it seem it stopped for some reason. Does anybody have ideas on what is going on?

[Thu Jul 19 11:38:15 2012] Beginning transcriptome assembly merge
-------------------------------------------

[Thu Jul 19 11:38:15 2012] Preparing output location Documents/RNA_Seq/LSD1_analysis_072012/cuffmerge_07172012//
[Thu Jul 19 11:38:17 2012] Converting GTF files to SAM
buszczak-macpro:~ zwang$