EPI2ME Labs Pangolin does not appear to Update Pangolin when checking "Update Data"

Question

EPI2ME Labs Pangolin does not appear to Update Pangolin when checking "Update Data"

mgurbano opened this issue 3 months ago · 5 comments

Ask away!

Good Morning All,
First off I am a huge fan of wf-artic and this pre-packaged analysis software.
I have always selected the check box within EPI2ME labs to "update data" [which says it updates Pangolin and Nextclade data at runtime] every time I run analysis. I was wondering why it never updated my Pangolin from version 4.1.3 to version 4.3 as I assumed it would have been. Am I understanding something incorrectly here? I have recently updated the wf-artic workflow and now I am on Pangolin version 4.3 as a result of that update, but I had thought I was constantly up to date because of this check box. Any info would be appreciated!
Best,
Matt

Answer 1 · 2024-08-15T15:25:32.000Z

Update: when I look at an analyzed run, it says that I was running Pangolin Version 4.3.1 and Pangolin Data Version 1.29, which are the most up to date versions. Does this mean that it was actually updating and running the correct versions, but my Invocation logs were still saying I was using V4.1.3 because I hadn't updated the wf-artic workflow?

Answer 2 · 2024-09-17T10:50:26.000Z

Hi Matt,
Apologies for delay. Have you resolved the issue? If you can see pangolin-data version 1.29 in the HTML report's version table, you can be sure that Pangolin was updated at runtime, since the current container bundles an older version than this.

Versions of wf-artic prior to v0.3.31 released in August 2023 did not update Pangolin and Nextclade by default, so if you were using an old version of wf-artic you may not have generated up to date lineage calls (unless manually setting --update_data to true).

Thanks,
Bede

Answer 3 · 2024-09-18T19:33:07.000Z

Good Afternoon Bede, I had replied to my own comment on Aug 15th with the resolution. Thank you for the follow up! Best, Matt Urbano * * * * * * * Matthew Urbano Genomics Lead Scientist, Molecular Diagnostics Laboratory Fralin Biomedical Research Institute at VTC PCR/Seq Team Whole Genome Sequencing of SARS-CoV-2 * * * * * * *

…

________________________________ From: Bede Constantinides ***@***.***> Sent: Tuesday, September 17, 2024 6:50:48 AM To: epi2me-labs/wf-artic ***@***.***> Cc: Urbano, Matthew ***@***.***>; Author ***@***.***> Subject: Re: [epi2me-labs/wf-artic] EPI2ME Labs Pangolin does not appear to Update Pangolin when checking "Update Data" (Issue #112) Hi Matt, Apologies for delay. Have you resolved the issue? If you can see pangolin-data version 1.29 in the HTML report's version table, you can be sure that Pangolin was updated at runtime, since the current container bundles an older version than this. Versions of wf-artic prior to v0.3.31 released in August 2023 did not update Pangolin and Nextclade by default, so if you were using an old version of wf-artic you may not have generated up to date lineage calls (unless manually setting --update_data to true). Thanks, Bede — Reply to this email directly, view it on GitHub<#112 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A4H5WO54AWMI37V74FG7LC3ZXACQRAVCNFSM6AAAAABMSLPP5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJVGMYDIMRYGY>. You are receiving this because you authored the thread.

Answer 4 · 2024-09-18T19:35:54.000Z

Good Afternoon Bede, Upon reexamination, that is not the resolution that I included on Aug 15. I thought this was a different ONT github forum post on a quick scan. That is my fault. This situation has been resolved, though. It turned out that it was actually pulling the correct and most updated version, but in the software it looked like it wasn't! This has since been fixed with a newer version of EPI2ME Labs, I'm sorry that I can't remember which version update did it. Best, Matt Urbano * * * * * * * Matthew Urbano Genomics Lead Scientist, Virginia Tech Molecular Diagnostics Laboratory Fralin Biomedical Research Institute at VTC * * * * * * *

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________________________________ From: Urbano, Matthew ***@***.***> Sent: Wednesday, September 18, 2024 3:32 PM To: epi2me-labs/wf-artic ***@***.***>; epi2me-labs/wf-artic ***@***.***> Cc: Author ***@***.***> Subject: Re: [epi2me-labs/wf-artic] EPI2ME Labs Pangolin does not appear to Update Pangolin when checking "Update Data" (Issue #112) Good Afternoon Bede, I had replied to my own comment on Aug 15th with the resolution. Thank you for the follow up! Best, Matt Urbano * * * * * * * Matthew Urbano Genomics Lead Scientist, Molecular Diagnostics Laboratory Fralin Biomedical Research Institute at VTC PCR/Seq Team Whole Genome Sequencing of SARS-CoV-2 * * * * * * *

________________________________ From: Bede Constantinides ***@***.***> Sent: Tuesday, September 17, 2024 6:50:48 AM To: epi2me-labs/wf-artic ***@***.***> Cc: Urbano, Matthew ***@***.***>; Author ***@***.***> Subject: Re: [epi2me-labs/wf-artic] EPI2ME Labs Pangolin does not appear to Update Pangolin when checking "Update Data" (Issue #112) Hi Matt, Apologies for delay. Have you resolved the issue? If you can see pangolin-data version 1.29 in the HTML report's version table, you can be sure that Pangolin was updated at runtime, since the current container bundles an older version than this. Versions of wf-artic prior to v0.3.31 released in August 2023 did not update Pangolin and Nextclade by default, so if you were using an old version of wf-artic you may not have generated up to date lineage calls (unless manually setting --update_data to true). Thanks, Bede — Reply to this email directly, view it on GitHub<#112 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A4H5WO54AWMI37V74FG7LC3ZXACQRAVCNFSM6AAAAABMSLPP5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJVGMYDIMRYGY>. You are receiving this because you authored the thread.

Answer 5 · 2024-09-19T10:05:48.000Z

Hi Matt,
I'm glad to hear you've resolved this – thanks for following up.

Best,
Bede