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Old 05-30-2012, 06:56 AM   #1
wangli
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Default 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.
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Old 06-08-2012, 03:26 PM   #2
kriskris
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I have the same problem! Did you ever find a fix?
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Old 06-08-2012, 03:52 PM   #3
wangli
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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
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Old 06-08-2012, 04:24 PM   #4
kriskris
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Thanks wangli, but that doesn't appear to be the problem. Any other ideas?
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Old 06-08-2012, 04:35 PM   #5
wangli
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you can look into the following thread:
http://seqanswers.com/forums/showthread.php?t=15092
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Old 07-19-2012, 09:08 AM   #6
zhwang
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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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