Memory issue when running test install script

[ghost]

Describe the bug A clear and concise description of what feature is not working.

Good afternoon. I am running the test script from the github page. I am getting the following error:

Impact Unable to complete test install of PHoenix

To Reproduce Steps to reproduce the behavior: I am working on a local machine. Phoenix version 2.0.0

Expected behavior Complete test script

Screenshots

[jvhagey]

Hi @bdelavan can you provide some information on what group you are with and the specs of the machine you are using? This isn't a bug, there are min memory requirements and your machine does not have enough memory as the error states. I would try passing --max_memory 10GB

Alternatively, you could go into the conf file and reduce the memory for the BBDuk steps here and here to 6GB and see if it runs. The SPAdes and PROKKA steps are the other steps that will be a bit of a memory hogs and I am unsure if it will finish with less memory.

Keep in mind that even if the Test profile runs to completion actually isolate files will require more memory as the test sample is a pretty small sample that is just meant to test the system. Let me know it goes and thanks for trying PHoeNIx! Lastly, I would use the 2.0.2 version as the last number is lets you know there was a patch to deal with bugs :)

[ghost]

Thank you for the quick response!

I am with the Arkansas Department of Health.

Here are the specs:

@.***

From: Jill V. Hagey, PhD @.> Sent: Friday, September 1, 2023 3:07 PM To: CDCgov/phoenix @.> Cc: Brian Delavan @.>; Mention @.> Subject: Re: [CDCgov/phoenix] Memory issue when running test install script (Issue #121)

Hi @bdelavanhttps://github.com/bdelavan can you provide some information on what group you are with and the specs of the machine you are using? This isn't a bug, there are min memory requirements and your machine does not have enough memory as the error states. I would try passing --max_memory 10GB

Alternatively, you could go into the conf file and reduce the memory for the BBDuk steps herehttps://github.com/CDCgov/phoenix/blob/e4dd6018420f315285106e970de2a3103eb1e253/conf/base.config#L72 and herehttps://github.com/CDCgov/phoenix/blob/e4dd6018420f315285106e970de2a3103eb1e253/conf/base.config#L78 to 6GB and see if it runs. The SPAdes https://github.com/CDCgov/phoenix/blob/e4dd6018420f315285106e970de2a3103eb1e253/conf/base.config#L90 and PROKKA https://github.com/CDCgov/phoenix/blob/e4dd6018420f315285106e970de2a3103eb1e253/conf/base.config#L102 steps are the other steps that will be a bit of a memory hogs and I am unsure if it will finish with less memory.

Keep in mind that even if the Test profile runs to completion actually isolate files will require more memory as the test sample is a pretty small sample that is just meant to test the system. Let me know it goes and thanks for trying PHoeNIx! Lastly, I would use the 2.0.2 version as the last number is lets you know there was a patch to deal with bugs :)

- Reply to this email directly, view it on GitHubhttps://github.com/CDCgov/phoenix/issues/121#issuecomment-1703266845, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AV36PGX24FAREIFQKX6FBATXYI56VANCNFSM6AAAAAA4H7NQ4Y. You are receiving this because you were mentioned.Message ID: @.**@.>>

[ghost]

I can get more RAM installed. We are really wanting to use the PHOENIX program.

From: Jill V. Hagey, PhD @.> Sent: Friday, September 1, 2023 3:07 PM To: CDCgov/phoenix @.> Cc: Brian Delavan @.>; Mention @.> Subject: Re: [CDCgov/phoenix] Memory issue when running test install script (Issue #121)

Hi @bdelavanhttps://github.com/bdelavan can you provide some information on what group you are with and the specs of the machine you are using? This isn't a bug, there are min memory requirements and your machine does not have enough memory as the error states. I would try passing --max_memory 10GB

Alternatively, you could go into the conf file and reduce the memory for the BBDuk steps herehttps://github.com/CDCgov/phoenix/blob/e4dd6018420f315285106e970de2a3103eb1e253/conf/base.config#L72 and herehttps://github.com/CDCgov/phoenix/blob/e4dd6018420f315285106e970de2a3103eb1e253/conf/base.config#L78 to 6GB and see if it runs. The SPAdes https://github.com/CDCgov/phoenix/blob/e4dd6018420f315285106e970de2a3103eb1e253/conf/base.config#L90 and PROKKA https://github.com/CDCgov/phoenix/blob/e4dd6018420f315285106e970de2a3103eb1e253/conf/base.config#L102 steps are the other steps that will be a bit of a memory hogs and I am unsure if it will finish with less memory.

Keep in mind that even if the Test profile runs to completion actually isolate files will require more memory as the test sample is a pretty small sample that is just meant to test the system. Let me know it goes and thanks for trying PHoeNIx! Lastly, I would use the 2.0.2 version as the last number is lets you know there was a patch to deal with bugs :)

- Reply to this email directly, view it on GitHubhttps://github.com/CDCgov/phoenix/issues/121#issuecomment-1703266845, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AV36PGX24FAREIFQKX6FBATXYI56VANCNFSM6AAAAAA4H7NQ4Y. You are receiving this because you were mentioned.Message ID: @.**@.>>

[ghost]

Issue resolved...need more memory on my end

[ghost]

Thank you for the quick response!

[jvhagey]

This discussion has details of laptops have worked to run PHoeNIx. We might have to work on making a custom config file as well.