Error for brie-count

[dipingxian431]

Hi
Thank you for the good tool.
I try to run the brie-count. But it returned with some error.

The code is :
brie-count -a /data/BRIE2/AnnoSE/SE.gff3 -s /data/outs/possorted_genome_bam.bam -b /data/outs/filtered_feature_bc_matrix/barcodes.tsv.gz -o out_dir -p 15

the report is:

example head cells:
['AAACAGCCAACTAGGG-1' 'AAACAGCCACCTGCTC-1' 'AAACAGCCAGGCTTCG-1'] ...
^M[BRIE2] loading gene annotations ... ^M[BRIE2] loading gene annotations ... Done.
This is not exon-skipping event: chr4:1003549:1003629:+@chr4:1004012:1003625:+@chr4:1004012:1004112:+!

So, what is the reason for it?
Thank you!

[dipingxian431]

I found I used the wrong gtf file. But I met a new error when I used the SE.gold.gtf.

brie-count -a /data/BRIE2/AnnoSE/SE.gold.gtf -s /data/outs/possorted_genome_bam.bam -b /data/outs/filtered_feature_bc_matrix/barcodes.tsv.gz -o out_dir -p 20

[BRIE2] example head cells:
['AAACAGCCAACTAGGG-1' 'AAACAGCCACCTGCTC-1' 'AAACAGCCAGGCTTCG-1'] ...
^M[BRIE2] loading gene annotations ... ^M[BRIE2] loading gene annotations ... Done.
[BRIE2] counting reads for 12586 genes in 9045 cells with 20 cores...
Can't find references 20 in samFile
Cannot fetch reads in region: None:38902668-38907054
Can't find references 10 in samFile
Cannot fetch reads in region: None:109873367-109877867

I tested both encode.v25 and encode.v27 files. The results are the same.

Thank you!