Freyja not giving the same output as standalone Freyja

[pratibha-kadam]

Hey There, I have observed that when I run Freyja in C-WAP pipeline and individual Freyja on my samples using same command it is giving me different abundance of variants.

So, I am not understanding why is it so even if the tool version is the same (1.3.11)

I am attaching the images for your reference

C-WAP pipeline

Freyja mix_plot.pdf

Thanks

[hughrandFDA]

Hi Pratibha, The person who is best placed to answer this is out this week (and next Monday is a holiday), so you are probably not going to get an answer to this until next week sometime. If this is critically urgent, let me know and I will see if someone else can find an answer for you. Hugh

From: Pratibha kadam @.> Sent: Tuesday, October 4, 2022 12:23 AM To: CFSAN-Biostatistics/C-WAP @.> Cc: Subscribed @.***> Subject: [EXTERNAL] [CFSAN-Biostatistics/C-WAP] Freyja not giving the same output as standalone Freyja (Issue #12)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

Hey There, I have observed that when I run Freyja in C-WAP pipeline and individual Freyja on my samples using same command it is giving me different abundance of variants.

So, I am not understanding why is it so even if the tool version is the same (1.3.11)

I am attaching the images for your reference

C-WAP pipeline

[Screenshot from 2022-10-04 09-41-17]https://secure-web.cisco.com/1zA-qda8PDvo2NdUOOZgimoZwfTY8gj_O6PDbNyu_tq_t8MtElwycyocs1HKdy2DM2X1m-TtKq2QM4KD_VAZ-BnrnNGGFLtDaYKOiq4xsM8ZljwZFzAJ9PbQBScMh8WpLAlhyBmp0COU7eg2JL09DHM8kUQBdNLs2Sg92ZSibFKY_tcTFT-sWoNrcqR6u2NHE/https%3A%2F%2Fuser-images.githubusercontent.com%2F88572259%2F193733500-9dc6702d-1ec9-4e2c-904d-ccd2dd06d6fb.png

Freyja mix_plot.pdfhttps://secure-web.cisco.com/1jMqN1fkt890y_SClMSKoBPOMeFdo2ooI4MGWdIsa8qJsOJSym1Lln2ryIdu1g8frEFdzK4FhTnyg2coqZ5_n31LR778MxGUQ7hawMNrWi_G4S6zFgS7B1jfzRduP3w3nsVz-evqXuv12nl-MhjlJsExef2gIOo7GYjc22k_trEh2ib_9aNP043AGFjc6yN0axF18b2HpV_-kSt1r4_PE_A/https%3A%2F%2Fgithub.com%2FCFSAN-Biostatistics%2FC-WAP%2Ffiles%2F9702763%2Fmix_plot.pdf

Thanks

— Reply to this email directly, view it on GitHubhttps://secure-web.cisco.com/1TGz6B2dQdoEggdyfd09EXW2mjWwUZNFhsC0MneD0pX075hYZCPjhzjZSGCI8jhnEaU5S00Jyp9_qIz9t_7bupm3Gtg0G07SPGvO3kER7DcBHqnD8OallvZf5o7QgFVC4Rf3ZRVYEDyPv2inMXgfdPem0xAlVrROHgaWe5MhG8VKkjh1kQPeOJPbpHTBUoALDXntKJ1dPrHZK0d8mhFp0LA/https%3A%2F%2Fgithub.com%2FCFSAN-Biostatistics%2FC-WAP%2Fissues%2F12, or unsubscribehttps://secure-web.cisco.com/1UKQzDJA8EZ_5fzg06rKSWSk5yXSxI9dORM9crOssL5PVOZKS18WiAToPB1wXBOebLA4qTh4fPWHGoCDIYPMCYENyswQ_F9y2PfS_0DS5xNhjsVkxvHU8Y_ouzOQ2FgSwyTAN3-GQErU7lv3BJmtw_Gq_yZPHR4vDojxOiWi9c-w7sxwLZOo3kPIbfSIGFAqTmAqiHa_6EyM8B5dq6xR4FA/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAB2BAG4KMGCJOV7TSRP35SDWBOWKFANCNFSM6AAAAAAQ4F4ZGQ. You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>

[pratibha-kadam]

It’s not an urgency for me. I will till then :)

Thank you Hugh

On Tue, 4 Oct 2022 at 6:39 PM, hughrandFDA @.***> wrote:

Hi Pratibha, The person who is best placed to answer this is out this week (and next Monday is a holiday), so you are probably not going to get an answer to this until next week sometime. If this is critically urgent, let me know and I will see if someone else can find an answer for you. Hugh

From: Pratibha kadam @.> Sent: Tuesday, October 4, 2022 12:23 AM To: CFSAN-Biostatistics/C-WAP @.> Cc: Subscribed @.***> Subject: [EXTERNAL] [CFSAN-Biostatistics/C-WAP] Freyja not giving the same output as standalone Freyja (Issue #12)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

Hey There, I have observed that when I run Freyja in C-WAP pipeline and individual Freyja on my samples using same command it is giving me different abundance of variants.

So, I am not understanding why is it so even if the tool version is the same (1.3.11)

I am attaching the images for your reference

C-WAP pipeline

[Screenshot from 2022-10-04 09-41-17]< https://secure-web.cisco.com/1zA-qda8PDvo2NdUOOZgimoZwfTY8gj_O6PDbNyu_tq_t8MtElwycyocs1HKdy2DM2X1m-TtKq2QM4KD_VAZ-BnrnNGGFLtDaYKOiq4xsM8ZljwZFzAJ9PbQBScMh8WpLAlhyBmp0COU7eg2JL09DHM8kUQBdNLs2Sg92ZSibFKY_tcTFT-sWoNrcqR6u2NHE/https%3A%2F%2Fuser-images.githubusercontent.com%2F88572259%2F193733500-9dc6702d-1ec9-4e2c-904d-ccd2dd06d6fb.png>

Freyja mix_plot.pdf< https://secure-web.cisco.com/1jMqN1fkt890y_SClMSKoBPOMeFdo2ooI4MGWdIsa8qJsOJSym1Lln2ryIdu1g8frEFdzK4FhTnyg2coqZ5_n31LR778MxGUQ7hawMNrWi_G4S6zFgS7B1jfzRduP3w3nsVz-evqXuv12nl-MhjlJsExef2gIOo7GYjc22k_trEh2ib_9aNP043AGFjc6yN0axF18b2HpV_-kSt1r4_PE_A/https%3A%2F%2Fgithub.com%2FCFSAN-Biostatistics%2FC-WAP%2Ffiles%2F9702763%2Fmix_plot.pdf>

Thanks

— Reply to this email directly, view it on GitHub< https://secure-web.cisco.com/1TGz6B2dQdoEggdyfd09EXW2mjWwUZNFhsC0MneD0pX075hYZCPjhzjZSGCI8jhnEaU5S00Jyp9_qIz9t_7bupm3Gtg0G07SPGvO3kER7DcBHqnD8OallvZf5o7QgFVC4Rf3ZRVYEDyPv2inMXgfdPem0xAlVrROHgaWe5MhG8VKkjh1kQPeOJPbpHTBUoALDXntKJ1dPrHZK0d8mhFp0LA/https%3A%2F%2Fgithub.com%2FCFSAN-Biostatistics%2FC-WAP%2Fissues%2F12>, or unsubscribe< https://secure-web.cisco.com/1UKQzDJA8EZ_5fzg06rKSWSk5yXSxI9dORM9crOssL5PVOZKS18WiAToPB1wXBOebLA4qTh4fPWHGoCDIYPMCYENyswQ_F9y2PfS_0DS5xNhjsVkxvHU8Y_ouzOQ2FgSwyTAN3-GQErU7lv3BJmtw_Gq_yZPHR4vDojxOiWi9c-w7sxwLZOo3kPIbfSIGFAqTmAqiHa_6EyM8B5dq6xR4FA/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAB2BAG4KMGCJOV7TSRP35SDWBOWKFANCNFSM6AAAAAAQ4F4ZGQ>.

You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>

— Reply to this email directly, view it on GitHub https://github.com/CFSAN-Biostatistics/C-WAP/issues/12#issuecomment-1266971225, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVDYCYYLUEQEG22CKEELHDDWBQUABANCNFSM6AAAAAAQ4F4ZGQ . You are receiving this because you authored the thread.Message ID: @.***>

--

Thanks and Regards Pratibha

[jasmine-amir]

Hello,

Thanks for choosing C-WAP!

C-WAP is currently using Freyja version 1.3.10 (not 1.3.11) but we do plan to update soon.

In the results posted here from C-WAP_Freyja and Freyja, they both seem to have about 90% BA.2.

Unfortunately, I cannot elaborate further without knowing more about the input data, parameters used, and other factors, however it is also possible that the Freyja params we applied for C-WAP are different. Please see parseFreyjaBootstraps.py and startWorkflow.nf (lines 533 - 584) for more info about the Freyja params and bootstrapping C-WAP uses when running Freyja.

In the meantime, we are further reviewing the code regarding the nomenclature.

Jasmine

[jasmine-amir]

Hi Pratibha,

I have two more pieces of info that may be useful:

(1) In getDisplayName.py, the "pangolin2WHO" variable does group some variants for our pie chart displays.

(2) It seems that, even within a single Freyja versions, there can be different database options. Their read me describes it more here, but it generally seems like they pull the latest lineages available on the day that a user runs freyja update.

Best, Jasmine