search

arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
309 stars 118 forks source link

comparation between l_merge.py and lumpy with mutiple samples #232

Closed ytguojian closed 6 years ago

ytguojian commented 6 years ago

Hi Ryan, I have used lumpyexpress and l_merge.py to get a final whole SV variant VCF file(named file1). And I also want to get a whole VCF file using lumpy running on multiple sample at the same time(named file2). Which is better? How many samples can lumpy run at the same time? I used 357 sample to get a file2 , but it failed Cheers, Jian

ytguojian commented 6 years ago

Hi Ryan, The lumpy showed 'Exited with exit code 130.', when I run it on multiple samples (about 357 samples). But when I run it on 10 samples, it succeed. Did that mean the lumpy can not run on much more samples? Waiting for your reply. Thanks.

Cheers, Jian

ryanlayer commented 6 years ago

Yes. 357 would quite a bit of RAM.

On Wed, Jan 17, 2018 at 1:14 PM, ytguojian notifications@github.com wrote:

Hi Ryan, The lumpy showed 'Exited with exit code 130.', when I run it on multiple samples (about 357 samples). But when I run it on 10 samples, it succeed. Did that mean the lumpy can not run on much more samples? Waiting for your reply. Thanks.

Cheers, Jian

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/arq5x/lumpy-sv/issues/232#issuecomment-358430331, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUWFlcjD9GGVUm4qIhvGPWn1am8Qdks5tLlTCgaJpZM4RgsQu .

-- Ryan Layer