Cellranger count: Found two feature definitions with the same ID

[capsellabursa]

Almost the same issue as #39 in cellranger-6.0.1 The issue occurs after successful work mkref during count, the GTF is custom, but based on an example from the best practices. The features gene don't have transcript_id

Here is the error:

Found two feature definitions with the same ID: 
(ID: b'rna-NC_020754.1:1..67'; name: rna-NC_020754.1:1..67; type: Gene Expression) and (ID: b'rna-NC_020754.1:1..67'; name: 
rna-NC_020754.1:1..67; type: Gene Expression). 
All feature IDs must be distinct.

And part of GTF:

NC_020754.1 StringTie_RefSeq    exon    1   67  .   +   .   gene_id "rna-NC_020754.1:1..67"; transcript_id "rna-NC_020754.1:1..67";
NC_020754.1 StringTie   gene    1   67  .   +   .   gene_id "rna-NC_020754.1:1..67";
NC_020754.1 StringTie   gene    67  1029    .   +   .   gene_id "s-rRNA"; Note "12SribosomalRNA"; gbkey "rRNA"; product "s-rRNA";
NC_020754.1 StringTie_RefSeq    exon    67  1029    .   +   .   gene_id "s-rRNA"; transcript_id "s-rRNA"; Note "12SribosomalRNA"; gbkey "rRNA"; product "s-rRNA";

How to fix this problem?

[capsellabursa]

@pryvkin10x

[pryvkin10x]

Hello,

Thanks for reaching out. In order to get a timely response to your issue, please reach out to support@10xgenomics.com and they'll help you out.

[trum994]

Hello - is there a solution to this you can share ?