Running too slow!
Closed this issue · 2 comments
- spladder version: 3.0.2
- Python version: 3.8.2
- Operating System: Linux
Description
Dear Andre:
When I tried to run 20 samples, which need about 3~4 days. The speed is so slow. I still have many samples to run, so I want to know how to speed up this programming.
The following is my bash script, I set 20 parallels :
gtfDir=gencode.v19.annotation.nochr.gtf
bam_path=bam_list.txt
output=/path/to/spladder
spladder build -o $output -b $bam_path -a $gtfDir --parallel 20 --set-mm-tag nM
### What I Did
Paste the command(s) you ran and the output.
If there was a crash, please include the traceback here.
Hello， I am the same with you !
but , I have another error ,could you help me ?
That is quite worry me !
Thank you for your feedback
For large cohorts, we recommend running in parallel across several machines:
https://spladder.readthedocs.io/en/latest/spladder_cohort.html
Other than that, I also recommend using --sparse-bam. This will pre-parse your alignment files and should greatly speed up the process of event calling and quantification.
Regarding the issue of no output events, I'd recommend lowering the confidence level (from the default 3) to 2 or 1.
Please re-open, if you think the issue still persists.
Best,
Andre