"ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file."

[Pedro Silva]

Hi,

I'm having trouble using featureCounts, the program crashes complaining about the GTF file but I can't understand what the problem is.

The files I'm using are the dog (CanFam3.1) reference genome and GTF annotation from NCBI RefSeq without any modification

Using either the standalone featureCounts executable (2.0.1) or the featureCounts functions in the Rsubread package (2.2.2) I get the same crash and error message:

ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
The specified gene identifier attribute is 'gene_id'
An example of attributes included in your GTF annotation is 'gene_id ""; transcript_id "unknown_transcript_1"; gbkey "tRNA"; product "tRNA-Phe"; exon_number "1"; '
The program has to terminate.

Any help would be appreciated.

[Yang LIAO]

As suggested in the screen output, the GTF annotation from NCBI RefSeq contains empty gene_id values. This is disallowed in featureCounts.

You may consider removing the lines with empty gene_id values. We hope to find a general solution to such issues in our next release.