[maker-devel] Non-unique top level ID

[hueytyng]

Hi Carson,

I ran MAKER using RNAseq as evidence (tophat+cufflinks). The gff file is
provided to Maker under "est_gff". Maker runs fine but there are a few
failed contigs, and these error messages in my log:

ERROR: Non-unique top level ID for 1:JUNC00010801:0
While this is technically legal in GFF3, it usually
indicates a poorly fomatted GFF3 file (perhaps you
tried to merge two GFF3 files without accounting for
unique IDs).  MAKER will not handle these correctly.

--> rank=2, hostname=safs-raijen
ERROR: Failed while prepare section files
ERROR: Chunk failed at level:12, tier_type:3
FAILED CONTIG:scaffold11129|size28423

I do see multiple IDs in my gff. I have 9 RNAseq samples, is the way I
merged them causing the error?
This is what I've done to prepare the gff:

1. merge cuffmerge output
cuffmerge -o <outputdir> -p 4 assembly_list.txt
cufflinks2gff3 merged.gtf > merged.gff

2. merge junctions

find -name "junctions.bed" -exec cat {} \; >> all_junctions.bed

tophat2gff3 all_junctions.bed > all_junctions.gff
3. combine cuffmerge and junctions

gff3_merge -o tophatandcufflinks.gff merged.gff all_junctions.gff

4. provide in opts file

est_gff=tophatandcufflinks.gff #EST evidence from an external gff3 file

Thank you

Jenny
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