-
Notifications
You must be signed in to change notification settings - Fork 3
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
ensemble error #17
Comments
Thanks for the report. This is a Java memory error, it looks like you specified |
I have try to reduce the file and I increase the memory. However I have this problems:
|
Thanks for the follow up. That's a pretty similar error about memory issues so is likely the same underlying cause. Does the machine have 45Gb of memory to allocate? If it's not that high memory of a machine it might be running out of memory to allocate to Java, leading to this error. Hope this helps. |
I have 47G of ram
|
Thanks for the comment. I'm not sure how to follow up, did specifying your available memory, 27Gb, work to resolve the issue? As you noted, if you're using the system memory for other processes it won't be available to java so you could run into memory problems. Hope this resolves it for you. |
Maybe the comand that I use it is wrong.. could you please check?
The comand are not the same I use up to know.
|
The files should be specified with spaces, not commas, so you want:
It doesn't split commas so treated that as one file it didn't find. Hope this helps. |
Thanks so much!! Now works for mutect2 and varscan but if I use also vardcit output
|
This error typically indicates the input VCF is not ordered correctly and there are some out of order blocks. This code doesn't handle any of this sorting, since that's done in the full bcbio pipeline if you need this kind of prep. Practically, I'd suggest using |
I am getting the following error when trying to run ensemble, any insight? 2017-Jun-27 15:54:34 -0400 d1p-hydrars04.ldi.lan ERROR [bcbio.variation.recall.main] - |
Kathleen; |
Thank you for your reply, I will check my files.
Kathleen
…Sent from my iPad
On Jun 28, 2017, at 8:00 AM, Brad Chapman <notifications@github.com<mailto:notifications@github.com>> wrote:
Kathleen;
Thanks for the report and sorry about the problem. Looking at the code I believe this could happen if one of the input files to ensemble calling is completely empty. Is that possible? If so, excluding that one (or fixing the file itself) should hopefully get things working cleanly.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#17 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AHmO-X_JyyUJgTTvoNKGOwC1xMYjbiIiks5sIkBDgaJpZM4NY8b5>.
|
I run on RHEL 5.5 and I have this error:
I set again the path now I have the right bcftools..
I have this error now
The text was updated successfully, but these errors were encountered: