MSNovelist - Internal Erorr

Giovanni911 commented 2 years ago

Hi, I am trying to employ MSNovelist with my own data to check how it works. I am using and .mgf file obtained filtering the .raw data (from thermo) with MZmine, then with the exported .mgf file, I run a normal Molecular Networking (METABOLOMICS-SNETS-V2) using the same parameters you used in the manuscript for clustering bryophytes dataset, finally, I downloaded the clustered data (.mgf). I tried to submit both to MSNovelist, but while the bryophytes dataset data was run correctly, my data showed this error Can you help me to understand why it happened?

Thank you in advance, Giovanni Error MSNovelist

Giovanni911 commented 2 years ago

Maybe this can help Error MSNovelist2

meowcat commented 2 years ago

Hi,

thanks for the interest. If the bryophyte dataset is working, but your data is not, I suspect there is a problem with the format or spectra.

How many spectra are you trying to run?
In the web interface, after upload, you should see a list of your spectra with precursor m/z and an "edit" button. Does this work, and do you see the spectra when you click "edit"? (Compare this to the bryophyte data, it should look and work the same way. If it doesn't, there's an import problem.)
Have you tried running a smaller subset of the spectra (using only a part of the mgf file)? Potentially, an error in the mgf file precludes the import. In theory GNPS data should work fine but maybe there are some special cases that cause issues I am not yet aware of.

meowcat commented 2 years ago

Two more questions:

Did you pull the docker or build it yourself?
Does the console window, from which you start MSNovelist, show any errors?

Giovanni911 commented 2 years ago

Thank you for the prompt reply

First comment: 1) My file contains 331 spectra (I can also attach it if needed). 2) Yes I see the spectra list where I can open one by one and edit them. 3) No, I did not since this is the smaller I have, but I will create a smaller one to try.

Second comment: 1) Yes I pulled the docker image from the Docker Hub repo. 2) Yes, here is the error, honestly I forgot to check it, and probably here is the issue, since probably during Mzmine manipulation I also allowed double-charged ions detection, so maybe changing this should work.

Ps. I have one more question. To run some data on MSNovelist, first I must clusterize them on GNPS? Or can I even run a .mgf directly exported from Mzmine?

[Uploading Powershell error.png…]() ,

Giovanni911 commented 2 years ago

I ran a smaller job on Mzmine allowing only single-charged ion detection (also checked the mgf manually), ran it on GNPS for clusterization, and tried to run it on MSNovelist, but here is the error I got. Then I restarted docker and PowerShell I connected again and it started the computation of the same .mgf file containing 28 spectra till the end, where it got stuck: Stuck giving this error due to csi-fingerid server connection I think: Error_Stuck

meowcat commented 2 years ago

Hi, well that seems strange, can you run it again? Maybe the CSI server was just down for a minute. It's very possible that doubly charged ions are a problem. If you send me the data (stravsmi@eawag.ch or attach, as you prefer) I can check it myself. You don't need to GNPS. Any MGF should work. I have to check if you can even use the SIRIUS/CSI:FingerID export from MzMine that also includes the MS1.

Giovanni911 commented 2 years ago

I sent the data to your mail. Bests Giovanni

meowcat / MSNovelist

MSNovelist - Internal Erorr #5