comparation between l_merge.py and lumpy with mutiple samples

[ytguojian]

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]

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]

Yes. 357 would quite a bit of RAM.

…

On Wed, Jan 17, 2018 at 1:14 PM, ytguojian ***@***.***> 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 <#232 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAlDUWFlcjD9GGVUm4qIhvGPWn1am8Qdks5tLlTCgaJpZM4RgsQu> .

-- Ryan Layer