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bactopia / bactopia

A flexible pipeline for complete analysis of bacterial genomes
https://bactopia.github.io
MIT License
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Quick Start failed at "bactopia datasets" #415

Closed xykb86 closed 1 year ago

xykb86 commented 1 year ago

I was trying to go through "Quick Start ". "mamba activate bactopia" command worked fine, but running "bactopia datasets" generated the following error message: what I should do?

2023-05-19 09:29:13:root:INFO - Setting up pre-computed Genbank/Refseq minmer datasets 2023-05-19 09:29:13:root:INFO - ./datasets/minmer/sourmash-genbank-k21.json.gz exists, skipping 2023-05-19 09:29:13:root:INFO - ./datasets/minmer/sourmash-genbank-k31.json.gz exists, skipping 2023-05-19 09:29:13:root:INFO - ./datasets/minmer/sourmash-genbank-k51.json.gz exists, skipping 2023-05-19 09:29:13:root:INFO - ./datasets/minmer/mash-refseq-k21.msh exists, skipping 2023-05-19 09:29:13:root:INFO - Setting up antimicrobial resistance datasets 2023-05-19 09:29:13:root:INFO - Setting up latest AMRFinder+ database External command failed with exit code 1!

Command: bash -c 'mv 2022-10-11.2/* amrfinderdb/'

Standard error: mv: cannot stat '2022-10-11.2/*': No such file or directory

rpetit3 commented 1 year ago

Hi @xykb86

Here is a workaround: https://github.com/bactopia/bactopia/issues/377#issuecomment-1385578774

Otherwise, it might be worth checking out my dev build here: https://github.com/bactopia/bactopia/issues/394

Let me know if these don't work!

rpetit3 commented 1 year ago

Hi @xykb86

I'm happy to report I have released version 3 of Bactopia. With this release, your issue should now be taken care of.

If not please feel free to reopen this issue or create a new one.

Thanks for using Bactopia! Robert