6.0.1 mkref error, similar to closed issue #125

[ArielPaulson]

Hi,

I am also running cellranger mkref and getting the "error detected in GTF file", however it is not related to duplicate gene IDs.

This is a GTF which indexed just fine with cellranger 2.1.0, but 6.0.1 can't handle it. Running the gtf_to_gene_index command directly gives the following output:

error: Error parsing GTF on line 488742 Line = 'LG6 gtfAddCDS:FRAME0:ORF004 stop_codon 9861794 9861795 . + transcript_id "XM_025241621.1"; gene_id "LOC112565816"; gene_name "LOC112565816"; exon_number "2"; tss_id "TSS24711"; p_id "P24500";' Error(([9, 116, 114, 97, 110, 115, 99, 114, 105, 112, 116, 95, 105, 100, 32, 34, 88, 77, 95, 48, 50, 53, 50, 52, 49, 54, 50, 49, 46, 49, 34, 59, 32, 103, 101, 110, 101, 95, 105, 100, 32, 34, 76, 79, 67, 49, 49, 50, 53, 54, 53, 56, 49, 54, 34, 59, 32, 103, 101, 110, 101, 95, 110, 97, 109, 101, 32, 34, 76, 79, 67, 49, 49, 50, 53, 54, 53, 56, 49, 54, 34, 59, 32, 101, 120, 111, 110, 95, 110, 117, 109, 98, 101, 114, 32, 34, 50, 34, 59, 32, 116, 115, 115, 95, 105, 100, 32, 34, 84, 83, 83, 50, 52, 55, 49, 49, 34, 59, 32, 112, 95, 105, 100, 32, 34, 80, 50, 52, 53, 48, 48, 34, 59], IsNot))

I have no idea what to make of this.

Thanks, Ariel

[ArielPaulson]

Apparently this is the most complicated way to say "the phase value is missing". I got it fixed.