[maker-devel] Maker failing on reannotation due to duplicate toplevel ids

[Mikael Brandström Durling]

Hello all,

I'm running Maker (2.26 / r956 from svn) with a previous run in the input as maker_gff. However, the maker mpi ranks quit stop one after another with the following error messages.

prepare section files
Gathering GFF3 input into hits - chunk:3
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=4, hostname=my-mgrid2
ERROR: Failed while prepare section files
ERROR: Chunk failed at level:12, tier_type:2
FAILED CONTIG:scf_89936

In the end no ranks are running, but maker doesn't quit.

Checking the maker_gff input, I do find duplicated ids, as this sample:

scf_89779	snap_masked	match	3327927	3330228	82.61	+	.	ID=scf_89779:hit:158:33_0;Name=snap_masked-scf_89779-abinit-gene-33.92-mRNA-1
scf_89779	est_gff:cufflinks	expressed_sequence_match	3381415	3383015	113.082870	+	.	ID=scf_89779:hit:158:33_0;Name=1:CR_CR_17.8567.1;score=113.082870

but not for the scaffold found in the error message above. Are those two errors unrelated?

If I run maker without providing a maker_gff the run works fine.

Any input on this issue would be appreciated as I would like the reannotation to work in order to carry forward human readable names. 

cheers,
Mikael




-------------------------------------
Mikael Brandström Durling, PhD
Assistant Professor

Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences

Uppsala BioCenter
Dept of Forest Mycology and Plant Pathology
Box 7026, 75007 Uppsala
Visiting address: Almas Allé 5
Telefon: 018-671503
mikael.durling at slu.se, www.slu.se/mykopat