Error message in cuffcompare

[Line]

Hello,

I am trying to run cuffcompare with the transcript_GTF file from cufflinks but I get this error message:
Error: no ID found for GFF record start
Could you please help me with this? Thanks!!

[Rodri]

I'm running cuffcompare with the same problem. I think that the problem is in the GTF-file but I'm not really sure. Do you know how to do?

Thanks for your aid.

Hello,

I am trying to run cuffcompare with the transcript_GTF file from cufflinks but I get this error message:
Error: no ID found for GFF record start
Could you please help me with this? Thanks!!

[Jane M]

Hello,

If it can help, I ran Cuffcompare with this command line :

cuffcompare -r /path/both.reference.alternative.isoform.gff -V -R /path/Cufflinks/L2/transcripts.gtf

where transcripts.gtf is one of the output files of Cufflinks and both.reference.alternative.isoform.gff is like this :

##gff-version	3
DS571145	alternativeSplicer	gene	3484	4143	.	-	.	ID=EHI_151170;Name=hypothetical protein;
DS571145	alternativeSplicer	mRNA	3484	4143	.	-	.	ID=EHI_151170.ref;Name=EHI_151170.ref;Parent=EHI_151170;completeORF=yes
DS571145	alternativeSplicer	exon	3484	4143	.	-	.	ID=exon_EHI_151170.ref-1;Name=exon;Parent=EHI_151170.ref;
DS571145	alternativeSplicer	mRNA	3484	4143	.	-	.	ID=EHI_151170.alt1;Name=EHI_151170.alt1;Parent=EHI_151170;completeORF=no
DS571145	alternativeSplicer	exon	3484	3943	.	-	.	ID=exon_EHI_151170.alt1-1;Name=exon;Parent=EHI_151170.alt1;
DS571145	alternativeSplicer	exon	3997	4143	.	-	.	ID=exon_EHI_151170.alt1-2;Name=exon;Parent=EHI_151170.alt1;
DS571145	alternativeSplicer	gene	4256	5944	.	+	.	ID=EHI_151180;Name=calcineurin catalytic subunit A putative;
DS571145	alternativeSplicer	mRNA	4256	5944	.	+	.	ID=EHI_151180.ref;Name=EHI_151180.ref;Parent=EHI_151180;completeORF=yes
DS571145	alternativeSplicer	exon	4256	5944	.	+	.	ID=exon_EHI_151180.ref-1;Name=exon;Parent=EHI_151180.ref;

[Aholton]

Bump having this problem too