gpertea
An error message in stringtie's mix option
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.
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!
Thank you for your advice! I will rerun it using the latest version, and I'll provide feedback promptly.
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?
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 (@ [email protected]) ? 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.
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 (@ [email protected]) ? 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.
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:
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:
There is my parameters:
#SBATCH -N 1 #SBATCH -n 1 #SBATCH --ntasks-per-node=56 #SBATCH -o %j.output #SBATCH -e %j.error