SIRIUS-FBMN merge

[Scott Jarmusch]

Running into this error when running the merge workflow in online notebook...

Scott

[Kyo Bin Kang]

Hi Scott,

I guess it happened because CSI:FingerID did not provide any match, but this is only a simple guess without any clue, you know.

Kyo Bin

Kyo Bin Kang, PhD

Assistant Professor

College of Pharmacy, Sookmyung Women's University

Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, Korea

Tel: +82-2-2077-7103. Mobile: +82-10-8836-8839

https://kyobinkanglab.org

2022년 8월 2일 (화) 오후 11:49, Scott Jarmusch <scottja...@gmail.com>님이 작성:

Running into this error when running the merge workflow in online notebook...

Scott

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[Scott Jarmusch]

Hi Kyo Bin,

I think you are spot on. I went back and check the SIRIUS summaries and there is nothing in those summaries...Now if I understand SIRIUS, it should be successfully predicting formula, so something else to sort out :)

Scott

[Stefano Papazian]

I reported the same issue some months ago. 

And I do get results when I run SIRIUS on my computer for the same mgf 

Stefano Papazian
Head of National Facility for Exposomics
Metabolomics Platform, Science for Life Laboratory | SciLifeLab
Department of Environmental Science (ACES) | Stockholm University, Sweden
https://www.scilifelab.se/units/exposomics/
   

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[Scott Jarmusch]

Daniel Petra’s replied to me on Twitter…

“ @Ming correct me if I am wrong, but there where some issue with licensing and it also only supported MF calculations through SIRIUS. I guess @boeckerlab agrees that your best bet is to use the SIRIUS standalone (GUI). It is quiet fast and should run full data sets on a regular PC”

So just running through SIRIUS 5 and ignoring the GNPS workflow and merge 

Sent from my iPhone

On Aug 3, 2022, at 2:08 PM, Stefano Papazian <stefano....@scilifelab.se> wrote:



[Stefano Papazian]

Yes, that is basically what I am already doing. 

In the future it would be wonderful a similar NAP/GNPS workflow based on SIRIUS, which takes advantage of the network topology to re-rank candidates

[Samuel Stewart Bassett]

Hi Scott,

How did you go about merging your GNPS network with your SIRIUS annotation? With the integrated workflow no longer functional I'm wondering what the best approach is. After looking at the output summary files from SIRIUS it doesn't seem like there is a very good column to use to map the results onto the FBMN .graphml coming from GNPS. Any tips would be much appreciated.

Thanks,

Sam