search

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
361 stars 76 forks source link

An error message in stringtie's mix option #420

Open YIGUIz opened 3 months ago

YIGUIz commented 3 months ago

Hello, When I use the -mix parameter, I consistently encounter an error message that says "Segmentation fault". Can you give me some advice?

the parameters are the following:

stringtie -o Mammary.Gland_3_mix.out.gtf --mix -p 36 -G Bos_taurus.ARS-UCD1.3.111.gtf --rf Mammary.Gland_3Aligned.sortedByCoord.out.bam Mammary.Gland_3.sorted.bam

Looking forward to your response. Thank you very much.

gpertea commented 3 months ago

As I mentioned in #406, could you please try 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 the example data so we can look into to the issue more closely. Thanks!

YIGUIz commented 3 months ago

Thank you for your advice! I will rerun it using the latest version, and I'll provide feedback promptly.

YIGUIz commented 3 months ago

As I mentioned in #406, could you please try 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 the example data so we can look into to the issue more closely. Thanks!

Unfortunately, the error message still exists in the latest version. I will package my data and share it with you. how can I share the data with you?

gpertea commented 3 months ago

Could you upload to a file sharing service like Google Drive, OneDrive or Dropbox or some other way that could share large files like these, and send me the link (@ geo.pertea@gmail.com) ? If that is not an option for you, email me (or let me know your preferred email) and I'll set up a way for you to upload the files for me.

YIGUIz commented 3 months ago

Could you upload to a file sharing service like Google Drive, OneDrive or Dropbox or some other way that could share large files like these, and send me the link (@ geo.pertea@gmail.com) ? If that is not an option for you, email me (or let me know your preferred email) and I'll set up a way for you to upload the files for me.

Ok, thank you for your help. I'll send you the link.

YIGUIz commented 3 months ago

As I mentioned in #406, could you please try 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 the example data so we can look into to the issue more closely. Thanks!

Hi, Geo. I checked my code and found an error in the previous alignment of SR RNA-Seq. The program reruns normally when I correct the error. Thank you for your help again!

I have another question about the running time of the mix analysis. One test sample analysis lasted about 8 hours which I set -p 56 parameter, But it seems that only occupied one thread. Is that right? the running statistics are following: image

YIGUIz commented 3 months ago

As I mentioned in #406, could you please try 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 the example data so we can look into to the issue more closely. Thanks!

Hi, Geo. I checked my code and found an error in the previous alignment of SR RNA-Seq. The program reruns normally when I correct the error. Thank you for your help again!

I have another question about the running time of the mix analysis. One test sample analysis lasted about 8 hours which I set -p 56 parameter, But it seems that only occupied one thread. Is that right? the running statistics are following: image

There is my parameters:

SBATCH -N 1

SBATCH -n 1

SBATCH --ntasks-per-node=56

SBATCH -o %j.output

SBATCH -e %j.error