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BUG: 'meta' preset is allowed by q2-assembly command assemble megahit despite 'meta' not being a preset option for megahit #98

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schaermi opened this issue Aug 19, 2024 · 0 comments
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Describe the bug
The documentation for the qiime assembly plugin lists 'meta' as an option for the flag --p-presets. When this option is used, the user receives an error message stating that meta is an invalid preset for megahit.

To Reproduce
Steps to reproduce the behavior:

  1. Execute the command qiime assembly assemble-megahit with the flag --p-presets 'meta':
    qiime assembly assemble-megahit --i-seqs mysequences.qza --p-presets 'meta' --o-contigs mycontigs.qza --verbose
  2. Read stdout and stderr output

Expected behavior
I thought 'meta' was a standard preset for metagenomic data in megahit which would produce a .qza artifact containing contigs,

Please complete the following information:

  • OS: Ubuntu 22.04.4 LTS
  • QIIME 2 version: 2024.5 Metagenome Distribution

Additional context
I encountered this error while working on the Euler cluster.

@schaermi schaermi added the bug Something isn't working label Aug 19, 2024
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