Segmentation fault (core dumped) and problems of gene orientations

[Cesnl]

When I use the -mix parameter, I consistently encounter an error message that says "Segmentation fault (core dumped)." However, when I run StringTie separately with either short read BAM or long read BAM files, I don't receive any errors. What could be the reason for this? Additionally, I'd like to inquire why the gene orientations represented as '+' and '-' in the output GTF file from StringTie using short read BAM files are completely opposite to those in the reference annotation GTF.

[Cesnl]

Looking forward to your response. Thank you very much.

[YIGUIz]

hi, I met the same error. Did you solve this problem? Can you give me some advice?

the parameters are the following:

stringtie -o Mammary.Gland_3_mix.out.gtf --mix -p 12 --rf Mammary.Gland_3Aligned.sortedByCoord.out.bam Mammary.Gland_3.sorted.bam

Thank you for your help!

[gpertea]

Could you please try to the latest version (v2.2.2) just posted a couple of days ago, and if you still encounter the error it would be great if you can provide some example data so we can look into to the issue more closely. Thanks!