Error: prokka: Failed to download resource "aragorn"

[AnnaaaaaaaaV]

Hi everyone! I am new to this field and currently in the process of installing Prokka on my MacBook M2. Despite my attempts using both Homebrew and Conda package managers, the result is the same: Aragorn, a dependency of Prokka, is not available. I would greatly appreciate any assistance in resolving this matter !!

Error: prokka: Failed to download resource "aragorn" Failure while executing; /usr/bin/env /opt/homebrew/Library/Homebrew/shims/shared/curl --disable --cookie /dev/null --globoff --show-error --user-agent Homebrew/4.1.14\ \(Macintosh\;\ arm64\ Mac\ OS\ X\ 13.6\)\ curl/8.1.2 --header Accept-Language:\ en --retry 3 --fail --location --silent --head http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.38.tgz exited with 56. Here's the output: curl: (56) Recv failure: Connection reset by peer

[apcamargo]

Hi @AnnaaaaaaaaV

The problem is that there's no pre-compiled binary of Aragorn in Conda for Apple processors. You can try to following the installation instructions here: https://github.com/apcamargo/genomad/issues/36#issuecomment-1739385550

[AnnaaaaaaaaV]

Thank you very much for your advice. Unfortunately, even when trying to use the commands you suggested, I didn't get any results. The response is:

Could not solve for environment specs The following package could not be installed └─ prokka is not installable because it requires └─ aragorn >=1.2 , which does not exist (perhaps a missing channel).

[apcamargo]

What are the exact commands you are using?

[AnnaaaaaaaaV]

I’ve used the commands:

conda install mamba -c conda-forge conda config --add channels conda-forge conda config --add channels bioconda mamba install prokka

And I have obtained:

Looking for: ['prokka'] warning libmamba Could not parse mod/etag header bioconda/osx-arm64 (check zst) Checked 0.3s warning libmamba Could not parse mod/etag header bioconda/noarch (check zst) Checked 0.2s warning libmamba Could not parse mod/etag header warning libmamba Could not parse mod/etag header warning libmamba Could not parse mod/etag header pkgs/main/osx-arm64 (check zst) Checked 0.2s warning libmamba Could not parse mod/etag header pkgs/main/noarch (check zst) Checked 0.0s warning libmamba Could not parse mod/etag header pkgs/r/osx-arm64 (check zst) Checked 0.0s warning libmamba Could not parse mod/etag header pkgs/r/noarch (check zst) Checked 0.0s bioconda/osx-arm64 124.0 B @ 3.5kB/s 0.0s pkgs/main/osx-arm64 1.7MB @ 19.2MB/s 0.1s pkgs/r/noarch 1.1MB @ 8.5MB/s 0.0s pkgs/main/noarch 697.2kB @ 3.8MB/s 0.2s pkgs/r/osx-arm64 108.0 B @ 500.0 B/s 0.1s conda-forge/osx-arm64 6.8MB @ 24.0MB/s 0.3s conda-forge/noarch 12.1MB @ 35.6MB/s 0.3s bioconda/noarch 4.7MB @ 4.8MB/s 1.0s

Pinned packages:

• python 3.11.*

Could not solve for environment specs The following package could not be installed └─ prokka is not installable because it requires └─ aragorn >=1.2 , which does not exist (perhaps a missing channel).

Previously, I have used both:

brew install brewsci/bio/prokka conda install -c conda-forge -c bioconda -c defaults prokka

But the result was the same: Aragorn was not available.

Il giorno 7 ott 2023, alle ore 01:40, Antônio Camargo @.***> ha scritto:

What era the exact commands you are using?

— Reply to this email directly, view it on GitHubhttps://github.com/apcamargo/genomad/issues/41#issuecomment-1751503782, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BDCVRW7FAJB4P2FOWLIJBHTX6CJH5AVCNFSM6AAAAAA5VTXN6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJRGUYDGNZYGI. You are receiving this because you were mentioned.Message ID: @.***>

[apcamargo]

Can you try this:

mamba create -n prokka
mamba activate
conda config --env --set subdir osx-64
mamba install -c conda-forge -c bioconda prokka
mamba activate prokka

[AnnaaaaaaaaV]

Good morning! Thank you so much for the commands! They worked 😃, and I was able to install Prokka! Thank you very much for the support A

Il giorno 7 ott 2023, alle ore 16:39, Antônio Camargo @.***> ha scritto:

Can you try this:

mamba create -n prokka mamba activate conda config --env --set subdir osx-64 mamba install -c conda-forge -c bioconda prokka mamba activate prokka

— Reply to this email directly, view it on GitHubhttps://github.com/apcamargo/genomad/issues/41#issuecomment-1751728437, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BDCVRW5XQNTG5UXTOIRETBDX6FSSBAVCNFSM6AAAAAA5VTXN6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJRG4ZDQNBTG4. You are receiving this because you were mentioned.Message ID: @.***>

[apcamargo]

No worries :)

You might want to check out Bakta. As far as I know, Prokka is not being maintained anymore