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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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compound_identification.csv is missing #140

Closed Eli-Rousseau closed 10 months ago

Eli-Rousseau commented 10 months ago

Dear Sir/Madam,

I am currently working with the CLI on SIRIUS 5.8.3 to calculate the molecular formula and structure for my project. Also, I am only interested in the formula and structure of a specific group of compounds. Therefore, I decided to create my own database, using the standalone tool custom-db, which I saved in a working directory. The problem I am encountering is that after running the job and looking at all the file summaries at the project level, I am unable to retrieve the compound_identification.csv file which should have the results of my molecular structures.

This is a representation of the command that I used for my job:

/home/elrou/miniconda3/bin/sirius --input /home/elrou/InputFolder/mgf_files/Fragment_Database.mgf --output /home/elrou/OutputFolder/SiriusProjectSpace/ --recompute formula --compound-timeout 360 fingerprint structure --database /home/elrou/Database/Smiles_Database/ write-summaries

Note that I make sure I am connected before starting the job.

Here also is another picture of the files that are stored after the job in my directory:

folder

When I check the files stored at the composition level, some (but not all) seem to have a structure_candidates.csv file, but they only contain a header without more information.

folder2

As a control, I also tried to repeat the job with a different built-in database, as in the following example:

/home/elrou/miniconda3/bin/sirius --input /home/elrou/InputFolder/mgf_files/Fragment_Database.mgf --output /home/elrou/OutputFolder/SiriusProjectSpace/ --recompute formula --compound-timeout 360 fingerprint structure --database pubchem write-summaries

But again, I end up with the same result: the compound_identification.csv file is still missing.

I am a new user of SIRIUS, so it is also possible that I have overlooked something in the program. If you would like more information about my problem, please feel free to let me know.

I look forward to your reply.

Eli Rousseau.

Eli-Rousseau commented 10 months ago

The problem is solved, I made a mistake by using the wrong input file.