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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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no formula_candidate.tsv OR structure_candidate.csv #119

Closed zmahnoor14 closed 1 year ago

zmahnoor14 commented 1 year ago

Hi SIRIUS team,

I have installed SIRIUS 5.6.3 CLI and GUI.

I cannot retrieve the proper output in the given output directory which was working fine with SIRIUS4.

To be sure I used the demo data Bicucullin.ms and ran both CLI and GUI separately. I saved the results from GUI in a directory. But I still dont receive the following three important files:

id/formula_candidate.tsv (id being the directory within the given output directory) id/structure_candidate.tsv canopus_summary.tsv

All the results appear fine in the GUI but I cannot retrieve above three files when I save the results as .sirius output. For CLI, I use the following command: sirius --input Bicuculline.ms --output Bicuculline.json formula fingerprint structure --database coconut canopus

Do you know if I am using the right command to get results from sirius, csi:fingerid and canopus? Or is the output directory structure changed in SIRIUS5? If its has changed, how can I access the information from the above three files automatically (e.g: with fixed file names and a read-able format)?

Thanks : )

Kind regards, Mahnoor

mfleisch commented 1 year ago

Hey Mahnoor, the summaries can now be written independently from the computation by a separate subtool. This allows to write them in different locations than the project data and easily rewrite them when needed. In the GUI it is even possible to select a subset of the data to write summaries from.

You can just extend you command like this: sirius --input Bicuculline.ms --output Bicuculline.json formula fingerprint structure --database coconut canopus write-summaries --output <OUTPUT_DIR>

If no output dir is given the summaties will be written to the project location (as in SIRIUS 4).

zmahnoor14 commented 1 year ago

Hey Markus,

perfect thanks problem solved with write-summaries : )

Kind regards, Mahnoor