cuffmerge - error reading ref.gtf

[crh]

Hi

Attempted to run cuffmerge and received the following error:

You are using Cufflinks v2.0.0, which is the most recent release.
Error: duplicate GFF ID 'Cre01.g000050.t1.2' encountered!
[FAILED]
Error: could not execute cuffcompare

I checked the ref.gtf file for the record and it is unique:

less Au10.2E.201009combined_ch.gtf|grep Cre01.g000050.t1.2
chromosome_1 AUGUSTUS transcript 8846 14517 0.09 + . Cre01.g000050.t1.2;
chromosome_1 AUGUSTUS tss 8846 8846 . + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS 5'-UTR 8846 9014 0.39 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS start_codon 9015 9017 . + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS initial 9015 12007 0.92 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS internal 12193 12546 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS internal 12744 12993 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS terminal 13249 13479 1 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS intron 12008 12192 1 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS intron 12547 12743 1 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS intron 12994 13248 1 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 9015 12007 0.92 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 12193 12546 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 12744 12993 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 13249 13479 1 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS stop_codon 13477 13479 . + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS 3'-UTR 13480 14517 0.21 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS tts 14517 14517 . + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";


cuffmerge command was:
cuffmerge -g Au10.2E.201009combined_ch.gtf -s ~ref.fa assemblies.txt

Ideas?

Charles

[marianaboroni]

I'm facing the same problem:

If I run:

[]$/cuffcompare -r file.gff transcripts.gtf
I have as output:
You are using Cufflinks v2.0.2, which is the most recent release.
Error: duplicate GFF ID 'Smp_212780.1' encountered!

But If I take a look on the gff file, there isn't a duplicate ID!

My file:

Schisto_mansoni.SC_0243 chado five_prime_UTR 112010 112657 . + . ID=Smp_212780.1:5UTR;Parent=Smp_212780.1
Schisto_mansoni.SC_0243 chado gene 112658 118829 . + . ID=Smp_212780
Schisto_mansoni.SC_0243 chado CDS 112658 112839 . + 0 ID=Smp_212780.1:exon:1;Parent=Smp_212780.1
Schisto_mansoni.SC_0243 chado CDS 115610 115757 . + 0 ID=Smp_212780.1:exon:2;Parent=Smp_212780.1
Schisto_mansoni.SC_0243 chado CDS 118662 118806 . + 0 ID=Smp_212780.1:exon:3;Parent=Smp_212780.1
Schisto_mansoni.SC_0243 chado CDS 120587 120594 . + 0 ID=Smp_212780.1:exon:4;Parent=Smp_212780.1
Schisto_mansoni.SC_0243 chado polypeptide 112658 118829 . + . ID=Smp_212780.1ep;Derives_from=Smp_212780.1;colour=2;timelastmodified=06.03.2012+04:56:35+GMT;feature_id=24739718
Schisto_mansoni.SC_0243 chado mRNA 112658 118829 . + . ID=Smp_212780.1;Parent=Smp_212780

Any Idea?

[smcinturf]

I think I am having this same issue. I get the error with out using the -g option, so I think that the duplicated entry is in one of the transcripts.gtf files?

[Sat Oct 13 09:32:54 2012] Preparing output location ./merged_asm/
[Sat Oct 13 09:33:37 2012] Converting GTF files to SAM
gtf_to_sam: /lib64/libz.so.1: no version information available (required by gtf_to_sam)
[09:33:37] Loading reference annotation.
Error: duplicate GFF ID 'MELO3C003194T2' encountered!
[FAILED]
Error: could not execute gtf_to_sam