I'm using maker since a while now, and I never got any issues about it. I recently tried to include some Augustus prediction inside the annotation process by changing the line :
augustus_species=fly as it was specified in some maker tutorial.
At the end of the process, only a dozens of all my contigs (between 500-600), were annotated, and all the rest failed. When I'm looking in the log file, here is what I got :
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=GP-Pan ERROR: Failed while prepare section files ERROR: Chunk failed at level:12, tier_type:3 FAILED CONTIG:Andromeda ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:Andromeda
When I tried to look for a solution on maker google groups, the error they got was not exactly the same as me, and the main reasons they suspected the failure was because of too long contig name, which is not my case as it worked without Augustus.
Do you see something obvious that I might have forgot while adding this augustus option ? Thanks for your help !