search

genome / pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
GNU General Public License v3.0
162 stars 90 forks source link

Pindel does not use all assigned CPUs #72

Open Madelinehazel opened 7 years ago

Madelinehazel commented 7 years ago

Hello,

I am trying to run Pindel with multithreading option --number_of_threads 24. However, Pindel only seems to use on average 6 processors, even though 24 are available. How can this be resolved?

Thank you, Madeline

liangkaiye commented 7 years ago

Part of the code in reading and sorting is not multi-threaded. Better cut the genome into pieces using -c Chris:start-end, then use 4 threads per region

Hello,

I am trying to run Pindel with multithreading option --number_of_threads 24. However, Pindel only seems to use on average 6 processors, even though 24 are available. How can this be resolved?

Thank you, Madeline

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/genome/pindel/issues/72, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AB9s-8-p4DEkvSIAPb71DKWdOj5AWpT8ks5sl9rIgaJpZM4PjCLf.