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

[Carson Holt]

You can get the fixed version by doing svn update inside the maker
directory.  I will be changing the download version to 2.27 on
yandell0lab.org, probably this weekend.

Thanks,
Carson





On 12-11-29 11:20 AM, "Mikael Brandström Durling" <mikael.durling at slu.se>
wrote:

>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	113.0
>82870	+	.	ID=scf_89779:hit:158:33_0;Name=1:CR_CR_17.8567.1;score=113.08287
>0
>
>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
>
>
>
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