[Sniwells]

Dear community,

I am trying to run cuffmerge as suggested in the Nature Protocol on Cufflinks, but on my data it gives me the following error message:

...
Comparing against reference file gencode.v14.annotation.gtf
You are using Cufflinks v2.0.2, which is the most recent release.
Error: duplicate GFF ID 'ENST00000361547.2' encountered!
        [FAILED]
Error: could not execute cuffcompare

The call is:

cuffmerge -o outputfolder/ -g gencode.v14.annotation.gtf -s hg19.fa -p 30 assemblies.txt

Does this corresponds a known bug in cufflinks somehow?

This looks like a regression in the alignment+GTF record bundling code in Cufflinks. If anybody here can produce a relatively small test set that consistently reproduces this issue, I'll fix it pronto. Sorry for the annoying bug...

Any assistance would be much appreciated.

Thanks!

[mgogol]

I'm having the same problem. Same version of cufflinks, same error message.

[EugeneID]

I get the same error from cuffcompare using the same version of cufflinks and the same annotation.

But everything work fine, when I
(1) use annotation from USCS Table Browser (GENCODE Genes V14), or
(2) preprocess the annotation by the gffread utility ( http://cufflinks.cbcb.umd.edu/gff.html ) or
(3) by cuffcompare ( http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff )

I prefer the last way, because cuffcompare (adding the tss_id and p_id attributes) comfortably renumbers genes and transcripts while keeping their old names (like gene_name "APOE")

[Brance]

I try to run both of the cufflinks-2.1.0.Linux_x86_64 and cufflinks-2.0.2.Linux_x86_64 to deal with the human RNA-seq, but failed with
"Error: duplicate GFF ID 'ENST00000361547.2' encountered!
[FAILED]
Error: could not execute gtf_to_sam". So I switch back to 0.8.4 , but it is so heartbroking that it failed and stoped when chr1 was even not finished. Thanks for your attention.

I just posted a pre-release build of Cufflinks 0.8.4 (svn r1370) that addresses this issue. I was able to locally reproduce the bug with Uwe's test set (thanks!), and the build I've posted corrects it (for me, anyways). Please let me know if this crops up again (ideally with another test download to reproduce it).

You should know before trying this build that it is an SVN snapshot and hasn't gone through the normal round of release testing, so you may run into other issues.

This build also includes additional assembler fixes and direct BAM file support. You can now supply BAM files as input to Cufflinks (SAM is still supported).

Please download one of the tarballs with "0.8.4" in the version tag from:

http://cufflinks.cbcb.umd.edu/downloads/

[santhilalsubhash]

Getting same duplicate GFF ID error with cufflinks-2.1.1

I ran cufflinks on guided mode with the following parameters. I am getting each exon as different transcript:

~/bin/cufflinks-2.1.1.Linux_x86_64/cufflinks -o ./cufflinks_out -p 20 -g gencode.v16.annotation.gtf -u --library-type fr-secondstrand -L novel_trans --overlap-radius 500 input.bam

Sample output generated by cufflinks for single transcript:
Attached: sample_transcript.txt


This is the transcript information in reference annotation file gencode.v16.annotation.gtf
Attached: sample_gencode.V16.annotation.gtf


When I ran cuffdiff using transcript generated by cufflinks:

~/bin/cufflinks-2.1.1.Linux_x86_64/cuffdiff -o ./cuffdiff -u --library-type fr-secondstrand -p 20 -L CNTRL,SAMPLE transcript.gtf CNTRL.bam SAMPLE.bam

I am getting this error:

[03:39:52] Loading reference annotation.
Error: duplicate GFF ID 'ENST00000361547.2' encountered!

Please help me if someone already got solution for this issue.