[maker-devel] maker_map_ids anomaly

[Mikael Brandström Durling]

Hi,

I'm trying to load maker annotations into JBrowse, however, the flat file loader can't parse the maker gff stating "parse error: orphans". Looking into one of the broken maker transcripts, it looks like below. Note that the two different mRNAs get the same ID, but a different name. The lines from maker_map_ids are pasted below too. This was a re-annotation run of a previous maker run, which was id_mapped before being used as maker_gff in the current run with model_pass=1 in order to preserve gene names. (btw, loading the unmapped initial maker run into jbrowse works fine.)

scf_89829       maker   gene    38002   41976   .       +       .       ID=CROS1_G00002820;Name=CROS1_G00002820;Note=Protein of unknown function;
scf_89829       maker   mRNA    38002   41976   .       +       .       ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=CROS1_T00002820_1,maker-scf_89829-augustus-gene-0.68-mRNA-1;_AED=0.01;_QI=436|1|1|1|0.5|0.33|3|1149|602;_eAED=0.01;Note=Protein of unknown function;
scf_89829       maker   mRNA    38611   41976   .       +       .       ID=CROS1_T00002820_2;Parent=CROS1_G00002820;Name=CROS1_T00002820_1;Alias=maker-scf_89829-augustus-gene-0.68-mRNA-2;_AED=0.06;_QI=125|1|1|1|0.5|0.33|3|1149|602;_eAED=0.06;Note=Protein of unknown function;
scf_89829       maker   exon    38002   38349   .       +       .       ID=CROS1_T00002820_1:exon:1745;Parent=CROS1_T00002820_1;
scf_89829       maker   exon    38872   39702   .       +       .       ID=CROS1_T00002820_2:exon:1746;Parent=CROS1_T00002820_2,CROS1_T00002820_2;
scf_89829       maker   exon    39762   41976   .       +       .       ID=CROS1_T00002820_2:exon:1747;Parent=CROS1_T00002820_2,CROS1_T00002820_2;
scf_89829       maker   exon    38611   38647   .       +       .       ID=CROS1_T00002820_2:exon:1748;Parent=CROS1_T00002820_2;
scf_89829       maker   five_prime_UTR  38002   38349   .       +       .       ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1;
scf_89829       maker   five_prime_UTR  38872   38959   .       +       .       ID=CROS1_T00002820_1:five_prime_utr;Parent=CROS1_T00002820_1;
scf_89829       maker   CDS     38960   39702   .       +       0       ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1;
scf_89829       maker   CDS     39762   40827   .       +       1       ID=CROS1_T00002820_1:cds;Parent=CROS1_T00002820_1;
scf_89829       maker   three_prime_UTR 40828   41976   .       +       .       ID=CROS1_T00002820_1:three_prime_utr;Parent=CROS1_T00002820_1;
scf_89829       maker   five_prime_UTR  38611   38647   .       +       .       ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2;
scf_89829       maker   five_prime_UTR  38872   38959   .       +       .       ID=CROS1_T00002820_2:five_prime_utr;Parent=CROS1_T00002820_2;
scf_89829       maker   CDS     38960   39702   .       +       0       ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2;
scf_89829       maker   CDS     39762   40827   .       +       1       ID=CROS1_T00002820_2:cds;Parent=CROS1_T00002820_2;
scf_89829       maker   three_prime_UTR 40828   41976   .       +       .       ID=CROS1_T00002820_2:three_prime_utr;Parent=CROS1_T00002820_2;


Related id map lines:

CROS1_G00002820 CROS1_G00002820
maker-scf_89829-augustus-gene-0.68-mRNA-1       CROS1_T00002820_1
CROS1_T00002820_1       CROS1_T00002820_2


and the command line for maker_map_ids:

maker_map_ids --prefix CROS1_ --abrv_gene G --abrv_tran T -suffix _ --iterate 1 CrosV1.maker.output/CrosV1.all.unmapped.gff > CrosV1.maker.output/CrosV1.id_map

thanks for any hints,
Mikael