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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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Error when storing custom db #138

Closed Eli-Rousseau closed 7 months ago

Eli-Rousseau commented 8 months ago

Good day everyone,

I am currently using the CLI of sirius 5.8.4. where I am trying to use the custom-db tool. Whenever I try to import my .tsv file with the following command:

sirius custom-db --import=database.tsv

I receive the following error message on my console:

SEVERE: error when storing custom db

When I try then to display the list of imported custom databases with this other command:

sirius custom-db --show

It indicates me the following:

==> No Custom database found!

I will provide you an additional screenshot as attachment. In any case, I very much look forward to your response, and hopefully you will be able to assist me.

Best regards, Eli Rousseau.

custom-db_error

joXemMx commented 8 months ago

Hi, looks to me like you are simply missing a login. Please make sure you are logged in before calling custom-db and see if the error remains.

Eli-Rousseau commented 8 months ago

Indeed I overlooked this detail, thanks for pointing it out. However, after successfully connecting to my account, I tried to use the custom-db tool with the same command as described in my last message:

sirius custom-db --import=database.tsv

And I still have the same error message:

SEVERE: error when storing custom db

But this time with a different exemption message (see below).

And when I try then to display the list of imported custom databases with this other command:

sirius custom-db --show

It indicates me the following:

==> No Custom database found!

Could you further help me out with this?

error message 2

Hryflow commented 7 months ago

The correct syntax is like: Sirius -i trans-1.tsv custom-db --import=/full/path/to/myDB

  1. while "-i" is indicate a global input, here is where you enter your tsv file. I put my file under SIRIUS main folder, i works well.
  2. "--import=" indicate the database you want to create. The "--import" parameter expects a full path. As my test, SIRIUS gui can recognize it automaticlly.
Eli-Rousseau commented 7 months ago

Thank you very much for your contribution @Hryflow. I did manage to save my custom database this time. I had overlooked to use syntax with the -i option in my command. So my problem is solved and herewith I will close this issue.

Best regards, Eli Rousseau.