cuffmerge error

wangli · 05-30-2012, 07:56 AM

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 · 06-08-2012, 04:26 PM

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

wangli · 06-08-2012, 04:52 PM

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 · 06-08-2012, 05:24 PM

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

wangli · 06-08-2012, 05:35 PM

you can look into the following thread:
http://seqanswers.com/forums/showthread.php?t=15092

zhwang · 07-19-2012, 10:08 AM

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$

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05-30-2012, 07:56 AM	#1
wangli Member Location: Texas Join Date: Apr 2012 Posts: 48	cuffmerge error 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.

06-08-2012, 04:26 PM	#2
kriskris Junior Member Location: California, USA Join Date: May 2012 Posts: 4	I have the same problem! Did you ever find a fix?

06-08-2012, 04:52 PM	#3
wangli Member Location: Texas Join Date: Apr 2012 Posts: 48	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

06-08-2012, 05:24 PM	#4
kriskris Junior Member Location: California, USA Join Date: May 2012 Posts: 4	Thanks wangli, but that doesn't appear to be the problem. Any other ideas?

06-08-2012, 05:35 PM	#5
wangli Member Location: Texas Join Date: Apr 2012 Posts: 48	you can look into the following thread: http://seqanswers.com/forums/showthread.php?t=15092

07-19-2012, 10:08 AM	#6
zhwang Junior Member Location: Dallas, TX Join Date: Apr 2011 Posts: 6	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$