Invalid option --output-strains for augur filter in latest Nextstrain update

[ArnieBerg]

I cloned the latest ncov of Nextstrain (3.0.3) from github (running the CLI environment in conda, Ubuntu) and when I run the snakefile for any example profile, I get to an 'augur filter' step that reports that the option '--output-strains' is invalid. When I check 'augur filter -h', sure enough, there is no '--output-strains' option listed.

Maybe I need to update the Nextstrain conda package? After much difficulty I got the latest version installed but it made no difference. Has this broken?

[jameshadfield]

What version of augur are you running @ArnieBerg? This functionality was released in augur v11.2.0 (via this commit). Working out what version of augur you are using is somewhat connected to how you are running the workflow -- are you running snakemake itself, nextstrain build or snakemake --use-conda (or something else)?

[ArnieBerg]

Hi James, Thanks for your prompt response. Augur reports it is at version 11.1.2, which explains the missing functionality. That begs the question as to why when I use the following installation sequence do I not get the current version? curl http://data.nextstrain.org/nextstrain.yml --compressed -o nextstrain.yml conda env create -f nextstrain.yml conda activate nextstrain npm install --global auspice To invoke the SARS-CoV-2 example, I use the suggested command: snakemake --cores 4 --profile ./my_profiles/example -p Cheers, Arnie Berg From: james hadfield ***@***.***> Sent: Tuesday, April 13, 2021 3:54 PM To: nextstrain/cli ***@***.***> Cc: Arnie Berg ***@***.***>; Mention ***@***.***> Subject: Re: [nextstrain/cli] Invalid option --output-strains for augur filter in latest Nextstrain update (#119) What version of augur are you running @ArnieBerg <https://github.com/ArnieBerg> ? This functionality was released in augur v11.2.0 (via this commit <nextstrain/augur@f80ae36> ). Working out what version of augur you are using is somewhat connected to how you are running the workflow -- are you running snakemake itself, nextstrain build or snakemake --use-conda (or something else)? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#119 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFQ724IXJNHUNXTHSTV6HY3TIS4ORANCNFSM424AMUTQ> . <https://github.com/notifications/beacon/AFQ724KUE3NOB76WCWLAC23TIS4ORA5CNFSM424AMUT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOGDJCJJI.gif>

[ArnieBerg]

Further information....I am running this in a WSL environment on a Windows machine, so I created a new Ubuntu distro, installed conda and then installed Nextstrain. This instance gave me a version 12.0 for augur.

In the original Ubuntu distro, I was unable to successfully update Nextstrain. I could not remove it through conda. I deleted the Nextstrain environment and re-installed it, but it would not give me augur 12.0.

This ticket can be closed.

[jameshadfield]

Sorry to hear about these troubles @ArnieBerg.

In terms of the nCoV repo we are maintaining a conda environment which enforce that the rules use the correct versions of dependencies (augur, mafft etc etc). If you run your build via snakemake --use-conda --cores 4 --profile ./my_profiles/example -p it should 🤞 just work. In the case which you update the nCoV repo, then the conda environment snakemake uses will also update as needed. cc @huddlej

Let us know if there are any other issues!