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GFF error when converting to binary #237

Closed francicco closed 2 years ago

francicco commented 2 years ago

Hi,

I'm trying to convert a gff3 file in its binary for to use it under jbrowse/apollo. The plain text file gff3 file I'm using it's like this

RPCZ01000001.1  annotation  gene    164112  168197  .   +   .   ID=Thar.Scf0000969G1;Name=Thar.Scf0000969G1
RPCZ01000001.1  annotation  mRNA    164112  168197  60  +   .   ID=Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1
RPCZ01000001.1  annotation  exon    164112  164159  60  +   .   ID=exon1_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  start_codon 164112  164114  60  +   .   ID=exon1_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  CDS 164112  164159  60  +   0   ID=cds_of_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  exon    166214  166523  60  +   .   ID=exon2_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  CDS 166214  166523  60  +   0   ID=cds_of_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  exon    167467  167584  60  +   .   ID=exon3_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  CDS 167467  167584  60  +   2   ID=cds_of_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  exon    167764  167871  60  +   .   ID=exon4_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  CDS 167764  167871  60  +   1   ID=cds_of_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  exon    168087  168197  60  +   .   ID=exon5_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  CDS 168087  168194  60  +   1   ID=cds_of_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  stop_codon  168195  168197  60  +   .   ID=exon5_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1

I sort it and compress it like this:

bgzip Test.gff && tabix -p gff Test.gff.gz

When I load it under Jbrowse the compressed gff returns me an error, while the same file in plain text looks just fine

Screenshot 2022-03-25 at 18 41 00

I don't understand what I'm doing wrong, and how I can fix it. Thanks a lot F