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

[Daniel Ence]

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<mailto: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<http://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<http://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

--

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