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EXCEPTION: Bio::Root::Exception #506

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bijendrabio opened this issue Oct 22, 2024 · 2 comments
Closed

EXCEPTION: Bio::Root::Exception #506

bijendrabio opened this issue Oct 22, 2024 · 2 comments

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@bijendrabio
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Hello,
I received a following error while converting gtf to gff3. Kindly suggest

agat_convert_sp_gxf2gxf.pl -g input.gtf > output.gff3

Error;
EXCEPTION: Bio::Root::Exception -------------
MSG: '.transcript_id "anno1.g123180.t1"; gene_id "g_183256";' is not a valid frame
STACK: Error::throw
STACK: Bio::Root::Root::throw
STACK: Bio::SeqFeature::Generic::frame

Regards,
B

@Juke34
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Juke34 commented Oct 22, 2024

Something is wrong in your file. Check the line. Containing '.transcript_id "anno1.g123180.t1"; gene_id "g_183256";'
You must have 9 columns tab separated

@bijendrabio
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Something is wrong in your file. Check the line. Containing '.transcript_id "anno1.g123180.t1"; gene_id "g_183256";' You must have 9 columns tab separated

Indeed. It was due to space error in gff3 as indicated in ERROR msg. Thanks @Juke34

@Juke34 Juke34 closed this as completed Oct 24, 2024
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