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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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Stuck at 100% when running on all data #166

Open HarryHung417 opened 1 week ago

HarryHung417 commented 1 week ago

Screenshot 2024-06-17 010647 I was running SIRIUS and CANOPUS on my ms/ms data for class prediction. The software stopped running at 100% of the main task, and at 35% for some of the 'fingerprint' steps. The last sentence in the log of the paused procedures says 'Invalidate existing Results and Recompute'. I am using SIRIUS 6.0.0 and is there a solution to this besides deleting the steps that are stuck? Screenshot 2024-06-17 011243

typewritermonkey commented 1 week ago

How long did you wait for your job? It looks like the Zodiac step takes the longest. I'll leave mine running today and check it again tonight. It should be able to run 4000 compounds without running out of javaheapspace I hope

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kaibioinfo commented 1 week ago

ZODIAC needs a lot of memory actually. We have to implement a low-memory solution for that... :/ It computes pairwise similarities between all compounds (so in your case 4000 x 4000) and build up a huge graph. In molecular networks like GNPS this graph is shrinked down a lot to make visualisation easier. We keep the large graph - so it gets quite memory hungry. If it's not doing anything for hours it might indeed run into infinite garbage collection :/

Maybe run ZODIAC only on a subset of good and decent features?

kaibioinfo commented 1 week ago

I would "cancel all" jobs and restart them. If you do not check the check "force recompute" in the compute dialogue it should only recompute the jobs that failed.

typewritermonkey commented 1 week ago

Is it still worth running Zodiac on 142 features?

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HarryHung417 commented 1 week ago

Thank you for the suggestions. I tried to remove ZODIAC and re-run the program. My only solution now is to go down a patch to SIRIUS 5.8 and it is working fine. I may try 6.0 again later