So I've seen this error crop up in the forums several times, but attempting to solve with the suggestions (find/replace within the gff file, use the -i option) doesn't seem to help...
When I run
htseq-count /media/lab/Glacier/Completed_RNAseq/12.sam pf5.gff
I get the error
Error occured in line 5200 of file pf5.gff.
Error: Failure parsing GFF attribute line
[Exception type: ValueError, raised in __init__.py:177]
Checking the gff line 5200 looks like this (and a few after)
NC_004129 img_core_v400 CDS 6045540 6045707 . + 0 gene_id=637322614;locus_tag=PFL_5279;product=aspartate 1-decarboxylase precursor; PanD
NC_004129 img_core_v400 CDS 6045954 6047618 . + 0 gene_id=637322615;locus_tag=PFL_5280;product=glucose-6-phosphate isomerase
NC_004129 img_core_v400 CDS 6047747 6049684 . + 0 gene_id=637322616;locus_tag=PFL_5281;product=acetyl-coenzyme A synthetase
NC_004129 img_core_v400 CDS 6049738 6050604 . + 0 gene_id=637322617;locus_tag=PFL_5282;product=hypothetical protein
NC_004129 img_core_v400 CDS 6050665 6051942 . + 0 gene_id=637322618;locus_tag=PFL_5283;product=acetyl-CoA acetyltransferase
I'm lost as to how to proceed- There doesn't seem to be any error with the file
When I run
htseq-count /media/lab/Glacier/Completed_RNAseq/12.sam pf5.gff
I get the error
Error occured in line 5200 of file pf5.gff.
Error: Failure parsing GFF attribute line
[Exception type: ValueError, raised in __init__.py:177]
Checking the gff line 5200 looks like this (and a few after)
NC_004129 img_core_v400 CDS 6045540 6045707 . + 0 gene_id=637322614;locus_tag=PFL_5279;product=aspartate 1-decarboxylase precursor; PanD
NC_004129 img_core_v400 CDS 6045954 6047618 . + 0 gene_id=637322615;locus_tag=PFL_5280;product=glucose-6-phosphate isomerase
NC_004129 img_core_v400 CDS 6047747 6049684 . + 0 gene_id=637322616;locus_tag=PFL_5281;product=acetyl-coenzyme A synthetase
NC_004129 img_core_v400 CDS 6049738 6050604 . + 0 gene_id=637322617;locus_tag=PFL_5282;product=hypothetical protein
NC_004129 img_core_v400 CDS 6050665 6051942 . + 0 gene_id=637322618;locus_tag=PFL_5283;product=acetyl-CoA acetyltransferase
I'm lost as to how to proceed- There doesn't seem to be any error with the file
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