Restart bs_align - Githubissues

BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data

http://pellegrini.mcdb.ucla.edu/BS_Seeker2/

MIT License

60 stars 25 forks source link

Restart bs_align #37

Open keckstrom opened 3 years ago

keckstrom commented 3 years ago

I am in the process of running bs_align on several samples, and even after splitting into read subsets it is taking a long time to run (very high coverage sequencing). The HPC at my university has a 1 week walltime, which for most samples is plenty, but a few jobs failed to finish in that time. Is there a way to restart those jobs at the point of failure, or does the entire command need to be run again?

Thanks, Korin

guoweilong commented 3 years ago

Here are some suggestions for your case. https://github.com/BSSeeker/BSseeker2#1-performance

Actually, cut the large file into small pieces and mapped them independently will speed up the processing. Then merge all bam files together.

Best, Weilong