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Old 05-27-2016, 12:37 PM   #1
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Location: Barcelona

Join Date: Apr 2016
Posts: 3
Question htseq-count ERROR in GFF File?

Hello guys,

I'm trying to do a summary of counts in I convert Fatq groomer to sam with Map with BWA for Illumina (Galaxy Version 1.2.3) with a camponotus floridanus genome and
now i have a sam file:

~98,000,000 lines, 24,027 comments
format: sam database?
BWA Version: 0.5.9-r16 BWA run on single-end data

And a gff3 file from

~190,000 lines
format: gff3 database?
uploaded gff3 file

When i do a summary of counts with htseq-count:

Fatal error: Unknown error occured
Error occured when processing GFF file (line 5 of file /galaxy-repl/main/files/016/000/dataset_16000531.dat):
Feature CFLO10001-RA does not contain a 'gene_id' attribute
[Exception type: ValueError, raised in count.

Thanks you everyone!
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bioinformatics help, gff, htseq-count, summary of counts, usegalaxy

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