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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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Run-time stop problem #202

Open ahawhasnail opened 1 month ago

ahawhasnail commented 1 month ago

Hi, I am a beginner in the Sirius software. I extracted 1494 compounds with the method of "find by auto-msms" using Agilent MassHunter qualitative software, then exported the list of compounds into a cef. file format and passed it into Sirius 6.0.5 for analysis. The first three attempts failed because the progress bar stopped after running for a certain amount of time. Just now I tried the same method again, the progress bar under the job menu was completed. However, the display on the page is “SiriusSubToolJob-211285 | rt30.508-p642.602 (623490135231699187)] ToolChain Job failed due to: java.lang.RuntimeException: Can't find a feasible solution: Solution is buggy ", and the code keeps saying "Could not load User image from token. Using placeholder instead." Why is this?

 Another question I would like to ask is, what type of processed data should be passed into Sirius? Were they all 1,494 compounds extracted after qualitative software analysis, a subset of compounds that could be matched to commercial libraries, or leftover compounds with no molecular notation? How do I balance data quality with speed? I sincerely look forward to your reply.

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MartinHoffmannJena commented 1 month ago

Hi,

Are you able to share the input file that prompted this bug ("solution is buggy")?

The user token error message is unrelated, we'll fix that as well.

Regarding your other question, please join the SIRIUS community here: https://matrix.to/#/#sirius-ms:gitter.im and we will answer them over there

Thank you!

ahawhasnail commented 1 month ago

Thank you for your reply. Is the input file you mentioned the cef file I passed into Sirius? I uploaded it as an attachment, please check it. CEF for Sirius.zip