[maker-devel] How to solve Non-unique top level ID error in Maker annotation pipeline ?

[Upendra Bhattarai]

Hi,

I am trying to run a second round of Maker annotation job with a SNAP trained file. However, when I try to pass maker_gff=maker.all.gff.file.from.the.first.round.gff. I get Non-unique top level ID errors for all the scaffolds.

maker_round_1_master_datastore_index.log shows failed reports for all the scaffolds.

I tried gff3_merge with and without -l flag, both gff3 files ended up giving the same error. I also tried gaas_maker_merge_outputs_from_datastore.pl and used maker_mix.gff file for maker_gff. It again fails with the same error.

When I grep non-unique id. It shows two hits one in `match` and the other in `match_part`.

I saw some tutorials not passing maker_gff on the second round of the maker. But when I do that number of gene models decreases.

I have posted my question in Biostar (https://www.biostars.org/p/9506971/), with the maker_opts.ctl and error messages.

Can someone help me, please?

Thank you,

Upendra