[maker-devel] MAKER contig: Non-unique top level ID

[Irina Armean]

Hi Daniel,

Thanks for the mail. Yes, that was one of the sources I considered, but as
the same input gff3 files have been successfully used in other maker runs,
I've excluded them from potential cause.
Believe it has to do with the collation of the expected 5 chunk gffs of the
scaffold2, have not had a confirmation or disapproval of this though.

Best wishes,
Irina



On Fri, Oct 24, 2014 at 2:51 PM, Daniel Ence <dence at genetics.utah.edu>
wrote:

>  Hi Irina,
>
>  Have you looked through your input for the duplicate IDs that the error
> talks about? It looks like some of your input files contain features with
> the same ID.
>
>  ~Daniel
>
>
>  On Oct 24, 2014, at 7:17 AM, Irina Armean <iarmean at ebi.ac.uk> wrote:
>
>  Dear all,
>
> I can't get a subset of contigs to finish, they keep failing.
>
> The log below is of a 519 992 long and max_dna_len=100000. No gff file is
> created. Just evidence_0.gff.an contains data (blast, protein2genome),
> the other 4 are empty (evidence_1, evidence_2, evidence_3, evidence_4).
>
>
> ...processing 30 of 32
>  ...processing 31 of 32
> total clusters:5 now processing 0
> flattening protein clusters
> prepare section files
> Gathering GFF3 input into hits - chunk:0
> ERROR: Non-unique top level ID for
> 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=NA, hostname=ebi3-202.ebi.ac.uk
> ERROR: Failed while prepare section files
> ERROR: Chunk failed at level:12, tier_type:3
> FAILED CONTIG:scaffold2
>
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:scaffold2
>
> examining contents of the fasta file and run log
>
>
>
> --Next Contig--
>
> Any suggestions much appreciated.
>
> Best wishes,
> Irina
>
> --
>
>  _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20141024/60e3323c/attachment-0003.html>