[maker-devel] maker_map_ids anomaly

[Carson Holt]

So does the problem occur immediately following the maker_map_ids step or
does it occur after running maker before the maker_map_ids step.  I ask so
I can identify if it is the maker_map_ids script I neeed to debug or
maker.  Could you send me the GFF3 file imediatley preceding the step
where the error originate.

Thanks,
Carson


On 13-01-22 2:56 AM, "Mikael Brandström Durling" <mikael.durling at slu.se>
wrote:

>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=C
>ROS1_T00002820_1,maker-scf_89829-augustus-gene-0.68-mRNA-1;_AED=0.01;_QI=4
>36|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=m
>aker-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
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