[maker-devel] Non-unique top level ID

[Carson Holt]

If you use gff3_merge with the -l flag, then it will check for non-unique
ID's and give new IDs to make them unique.  Also in general it is better
just to use the cufflinks results and exclude tophat results as they tend to
be very noisy and decrease the quality of the final models overall.

Thanks,
Carson


From:  hueytyng <cynsb1987 at gmail.com>
Date:  Sunday, May 4, 2014 at 7:58 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Non-unique top level ID

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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