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ssadedin / ximmer

Ximmer is a system for CNV calling on exome and targeted genomic sequencing
http://ssadedin.github.io/ximmer/
GNU Lesser General Public License v2.1
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create_analysable_targets not working #41

Open brianlucla opened 2 years ago

brianlucla commented 2 years ago

We had a GC overhead limit error in the create analysable target stage, which prompted us to take a look at the bpipe.log which is attached below. It seems like the analysable.bed file is being repeatedly updated/created which is causing the memory error. bpipe.log

Any help here would be appreciated. Thank you!

ssadedin commented 2 years ago

hi @brianlucla can I confirm, which branch are you using when running?

I am close to merging the 3.0-alpha-1 branch to master and there are a huge number of changes there. Not sure if it will fix your problem but it will be much easier to diagnose using the active codebase we're working on.

brianlucla commented 2 years ago

Hi,

I’m using the 3.0-alpha-1 in a virtual environment.

On Wed, Aug 3, 2022 at 4:34 AM Simon Sadedin @.***> wrote:

hi @brianlucla https://github.com/brianlucla can I confirm, which branch are you using when running?

I am close to merging the 3.0-alpha-1 branch to master and there are a huge number of changes there. Not sure if it will fix your problem but it will be much easier to diagnose using the active codebase we're working on.

— Reply to this email directly, view it on GitHub https://github.com/ssadedin/ximmer/issues/41#issuecomment-1203832594, or unsubscribe https://github.com/notifications/unsubscribe-auth/A2LCZDDH2WN7I5JTU4VEAZLVXJKN3ANCNFSM55M6AW6Q . You are receiving this because you were mentioned.Message ID: @.***>

ssadedin commented 2 years ago

@brianlucla - I've merged a bunch of the upstream work to 3.0-alpha-1 now, so you could try this out. There is a fix for the specific problem you ran into. Looking at your error message, however, I can see you were on a somewhat old version of that branch, and there have been quite a lot of changes, including moving a bunch of the directories around (mainly: things that were in eval have moved to the top level). It might be easier to set up from scratch again than try to adapt your existing install.