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sirius-ms / sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
GNU Affero General Public License v3.0
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sirius 4.8.2 --> sirius 5.8.3 #131

Closed oyileo closed 9 months ago

oyileo commented 10 months ago

Hi: I use the following command in sirius 4.8.3： sirius --maxmz=850 -i ../03-S12_Sirius-removev2/S12.list_clean.mgf -o ./sirius-test formula -c 50 -p orbitrap zodiac fingerid -d BIO canopus

but when I use the sam command in sirius 5.8.3, it prompt: Unmatched arguments from index 13: 'fingerid', '-d', 'BIO', 'canopus'

so, how shold I use the same command in sirius 5.8.3?

zmahnoor14 commented 9 months ago

Maybe it might work if you replace:

fingerid -d BIO canopus

with:

fingerprint structure --database bio canopus

OR

fingerprint structure --database bio compound-classes
mfleisch commented 9 months ago

@zmahnoor14 is right fingerprint prediction and structure db search have been split into separate tools.

Example commands are also available here: https://boecker-lab.github.io/docs.sirius.github.io/cli/#csifingerid-predicting-molecular-fingerprints-compound-tool

Further --help gives you an overview over all available subtools. For each subtool a more specific help message can be printed with e.g. fingerprint --help