Thank you for the reply.
I will try this annotation GIF when I get my local galaxy to function.
Have a good day,
Delong

________________________________
De : Jennifer Jackson [j...@bx.psu.edu]
Envoyé : 9 juillet 2013 14:30
À : Delong, Zhou
Cc : galaxy-u...@bx.psu.edu
Objet : Re: [galaxy-user] Cuffmerge error: duplicate GFF ID encountered

Hello Delong,

Duplicated GFF IDs are not permitted in reference annotation inputs for this 
tool suite. There are a few options.

1 - edit the file to remove/reduce the duplicates. There could be scientific 
consequences when doing this, so consider carefully.

2 - use another source. iGenomes is a recommended option. An added benefit is 
that these files contain additional attributes in the 9th field utilized by the 
tools, enabling full functionality. You can read about this in the "inputs" 
section for each tool in the manual, I'll link it below.

The human iGenomes gtf file is already in the public Main Galaxy instance in 
Shared Data -> Data Libraries -> iGenomes. Or, you can download the original 
data at the Cufflinks web site, extract the gtf, and load where ever you are 
using Galaxy (local, cloud, other public instance).

http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server
     Example → RNA-seq analysis tools.
http://cufflinks.cbcb.umd.edu/manual.html
http://cufflinks.cbcb.umd.edu/igenomes.html

Best,

Jen
Galaxy team


On 7/4/13 6:30 AM, Delong, Zhou wrote:

Hello,
I was doing a RNA analyse and I wished to compare the transcription and 
expression of two samples using a reference annotation, however this is the 
error message I got:

=====Quote=====
Error running cuffmerge.
[Thu Jul  4 07:32:59 2013] Beginning transcriptome assembly merge
-------------------------------------------

[Thu Jul  4 07:32:59 2013] Preparing output location cm_output/
[Thu Jul  4 07:34:07 2013] Converting GTF files to SAM
[07:34:07] Loading reference annotation.
[07:34:07] Loading reference annotation.
[Thu Jul  4 07:34:08 2013] Quantitating transcripts
You are using Cufflinks v2.1.1, which is the most recent release.
Command line:
cufflinks -o cm_output/ -F 0.05 -g 
/galaxy/main_pool/pool7/files/006/446/dataset_6446730.dat -q 
--overhang-tolerance 200 --library-type=transfrags -A 0.0 
--min-frags-per-transfrag 0 --no-5-extend -p 4 cm_output/tmp/mergeSam_fileIO17rb
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File cm_output/tmp/mergeSam_fileIO17rb doesn't appear to be a valid BAM file, 
trying SAM...
[07:34:08] Loading reference annotation.
[07:35:53] Inspecting reads and determining fragment length distribution.
Processed 33854 loci.


Map Properties:
        Normalized Map Mass: 8719.00
        Raw Map Mass: 8719.00
        Fragment Length Distribution: Truncated Gaussian (default)
                      Default Mean: 200
                   Default Std Dev: 80


[07:35:53] Assembling transcripts and estimating abundances.
Processed 33854 loci.
[Thu Jul  4 07:39:29 2013] Comparing against reference file 
/galaxy/main_pool/pool7/files/006/446/dataset_6446730.dat
You are using Cufflinks v2.1.1, which is the most recent release.
Error: duplicate GFF ID 'ENST00000361547.2' encountered!
        [FAILED]
Error: could not execute cuffcompare

======End quote======

The job goes well without the annotation reference.
The annotation file I used can be downloaded here:
ftp://ftp.sanger.ac.uk/pub/gencode/release_17/gencode.v17.annotation.gtf.gz

Can anyone help me please?
Thanks,
Delong

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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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