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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Resource control #208

Closed srx3001 closed 3 years ago

srx3001 commented 4 years ago

Hi I ran CNVnator on a relatively small bam file and get this error::

Resources requested (8 procs, 25 GB) are greater than maximum allowed (8 procs, 21.8220596313477 GB)))

Obviously it asks more than what I have but I dont remember any steps that give it a threading or RAM parameter. I am on a personal desktop with 8 cores / 24GB RAM and sadly dont have access to anything better. How can I tell it how many threads /RAM to use?

abyzov commented 4 years ago

Hi, this is the first time we see such an error. Could you elaborate which command you ran to get this message.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

On Jun 21, 2020, at 10:41 AM, Srdjan K notifications@github.com<mailto:notifications@github.com> wrote:

Hi I ran CNVnator on a relatively small bam file and get this error::

Resources requested (8 procs, 25 GB) are greater than maximum allowed (8 procs, 21.8220596313477 GB)))

Obviously it asks more than what I have but I dont remember any steps that give it a threading or RAM parameter. I am on a personal desktop with 8 cores / 24GB RAM and sadly dont have access to anything better. How can I tell it how many threads /RAM to use?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/abyzovlab/CNVnator/issues/208, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACLKGOKKYBHIKUEDL6BONUDRXYS37ANCNFSM4OD5C7OQ.

srx3001 commented 4 years ago

Hello,

I am really sorry, this was my mistake, the error was not generated by CNVnator, but the environment itself, it's just that the logs were a bit confusing. CNVnator works perfectly.

The issue should be closed, sorry for the inconvenience.

Srdjan

On Sat, Jun 27, 2020 at 6:22 AM abyzov notifications@github.com wrote:

Hi, this is the first time we see such an error. Could you elaborate which command you ran to get this message.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

On Jun 21, 2020, at 10:41 AM, Srdjan K <notifications@github.com<mailto: notifications@github.com>> wrote:

Hi I ran CNVnator on a relatively small bam file and get this error::

Resources requested (8 procs, 25 GB) are greater than maximum allowed (8 procs, 21.8220596313477 GB)))

Obviously it asks more than what I have but I dont remember any steps that give it a threading or RAM parameter. I am on a personal desktop with 8 cores / 24GB RAM and sadly dont have access to anything better. How can I tell it how many threads /RAM to use?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub< https://github.com/abyzovlab/CNVnator/issues/208>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ACLKGOKKYBHIKUEDL6BONUDRXYS37ANCNFSM4OD5C7OQ>.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/abyzovlab/CNVnator/issues/208#issuecomment-650488302, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFCKGCOAG4NDFZERNZR4NUDRYVXYTANCNFSM4OD5C7OQ .