[Gmod-help] Error: chr1 doesn't have a primary id

[Nigel Wilson]

Hi,

I am attempting to load 3 gff3 files into a postgres Bio::DB::SeqFeature::Store database using the bp_seqfeature_load.pl script that comes with bioperl.
My files are: chromosomes.gff3, ideogram.gff3 and study_2.gff3, being loaded in that order. The chromosomes.gff3 file loads without error. However, when I attempt to load either of the other 2 files, I receive the following error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: chr1 doesn't have a primary id
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:720
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:699
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:343
STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:354
STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:243
STACK: /usr/bin/bp_seqfeature_load.pl:135
-----------------------------------------------------------

I loaded the chromosomes.gff3 file with the following command:

bp_seqfeature_load.pl -d dbname=gbtest -a DBI::Pg -u xxx -p xxx -c -v chromosomes.gff3

And for the ideogram.gff3 and study_2.gff3 files, I use the commad:

bp_seqfeature_load.pl -d dbname=gbtest -a DBI::Pg -u xxx -p xxx -v <filename.gff3>

I have tried to correct this error by defining the regions using the ##sequence-region pragma, however that results in a duplication of the chromosome region in my database. Is there a way to allow loading of multiple gff3 files, whose parent IDs are already loaded into the database?

(P.S. program versions, example files are located past the signature)

Thanks

Nigel Wilson
_________________________________________________
Research Student
The Centre for Applied Genomics
The Hospital for Sick Children, MaRS Building - East Tower
*: 416.813.7032
*: 101 College St., Rm 14-701, Toronto, Ontario  M5G 1L7


Info

BioPerl Version -> latest bioperl-live
Gbrowse version: 2.10

File Examples:
Chromosomes.gff3

##gff-version 3
##Index-subfeatures 1

chr1    hg18    chromosome      1       247249719       .       .       .       ID=chr1;Name=Chr1
chr10   hg18    chromosome      1       135374737       .       .       .       ID=chr10;Name=Chr10
chr11   hg18    chromosome      1       134452384       .       .       .       ID=chr11;Name=Chr11
chr12   hg18    chromosome      1       132349534       .       .       .       ID=chr12;Name=Chr12

ideogram.gff3
##gff-version 3
##Index-subfeatures 1

chr1    UCSC    cytoband    1   2300000 .   .   .   Parent=chr1;Name=Cytoband:1p36.33;Alias=p36.33;stain=gneg;
chr1    UCSC    cytoband    2300001 5300000 .   .   .   Parent=chr1;Name=Cytoband:1p36.32;Alias=p36.32;stain=gpos25;
chr1    UCSC    cytoband    5300001 7100000 .   .   .   Parent=chr1;Name=Cytoband:1p36.31;Alias=p36.31;stain=gneg;
chr1    UCSC    cytoband    7100001 9200000 .   .   .   Parent=chr1;Name=Cytoband:1p36.23;Alias=p36.23;stain=gpos25;
chr1    UCSC    cytoband    9200001 12600000    .   .   .   Parent=chr1;Name=Cytoband:1p36.22;Alias=p36.22;stain=gneg;

study_2.gff3
##gff-version 3
##Index-subfeatures 1
chrX    DGV2    sample_level_variant    136348080   136348238   .   +   .   ID=abc_41;Parent=chrX;Name=abc_41;variant_type=CNV;gender=M;study=test 2009;
chr7    DGV2    sample_level_variant    7074153 7074960 .   +   .   ID=abc_4025;Parent=chr7;Name=abc_4025;variant_type=CNV;gender=M;study=test 2009;
chr2    DGV2    sample_level_variant    41069334    41070418    .   +   .   ID=abc_4023;Parent=chr2;Name=abc_4023;variant_type=CNV;gender=M;study=test 2009;
chr1    DGV2    sample_level_variant    71513720    71514441    .   +   .   ID=abc_3923;Parent=chr1;Name=abc_3923;variant_type=CNV;gender=M;study=test 2009;


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