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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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Custom-database CLI #106

Closed zmahnoor14 closed 4 weeks ago

zmahnoor14 commented 1 year ago

Hello SIRIUS developers,

I am currently using SIRIUS 5.6.3 CLI version and following the documentation: SIRIUS Documentation - Custom Database

so according to current documentation:

sirius --input /Users/mahnoor/SL_Sirius.tsv --name SL_Sirius custom-db --output /Users/mahnoor/SIRIUS

However, SIRIUS returns errors like: unknown options: "--input" or "output".

I think this needs an update as this command was working on SIRIUS4. Could you take a look into this issue?

Thanks, Mahnoor

simcoxkm commented 1 year ago

The custom database feature is also not working in the GUI. When I try to create a database by either typing in the SMILES code and hitting "open/create database" or by directly uploading a csv, I receive this error:

java.lang.NullPointerException: Name is null at java.base/java.lang.Enum.valueOf(Unknown Source) at de.unijena.bioinf.storage.blob.Compressible$Compression.valueOf(Compressible.java:44) at de.unijena.bioinf.storage.blob.CompressibleBlobStorage.of(CompressibleBlobStorage.java:40) at de.unijena.bioinf.chemdb.custom.CustomDatabase.open(CustomDatabase.java:99) at de.unijena.bioinf.chemdb.SearchableDatabases.loadCustomDatabaseFromLocation(SearchableDatabases.java:195) at de.unijena.bioinf.ms.gui.fingerid.custom_db.DatabaseDialog$ImportDatabaseDialog.lambda$runImportJob$2(DatabaseDialog.java:344) at de.unijena.bioinf.jjobs.LoadingBackroundTask$1.compute(LoadingBackroundTask.java:35) at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source)

Hope this helps!

my3sonsMN commented 11 months ago

Wondering if there has been a solution to the create custom database feature in the software. As others have commented the addition of smiles strings still doesn't seem to be working. would love to have a way to bring in exports from other databases to help build up the compounds thank you David Weil

gdiazcruz commented 9 months ago

Hello! I am having the same (or similar) issue with the 5.8.3 version:

java.lang.NullPointerException: Name is null at java.base/java.lang.Enum.valueOf(Unknown Source) at de.unijena.bioinf.storage.blob.Compressible$Compression.valueOf(Compressible.java:44) at de.unijena.bioinf.storage.blob.CompressibleBlobStorage.of(CompressibleBlobStorage.java:40) at de.unijena.bioinf.chemdb.custom.CustomDatabase.open(CustomDatabase.java:99) at de.unijena.bioinf.chemdb.SearchableDatabases.loadCustomDatabaseFromLocation(SearchableDatabases.java:195) at de.unijena.bioinf.ms.gui.fingerid.custom_db.DatabaseDialog$ImportDatabaseDialog.lambda$runImportJob$2(DatabaseDialog.java:349) at de.unijena.bioinf.jjobs.LoadingBackroundTask$1.compute(LoadingBackroundTask.java:35) at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source)

my3sonsMN commented 9 months ago

Do you think you can let me know when you have a solution.

Thank you

David weil

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From: gdiazcruz @.> Sent: Tuesday, September 12, 2023 5:31:14 AM To: boecker-lab/sirius @.> Cc: WEIL,DAVID (Agilent USA) @.>; Comment @.> Subject: Re: [boecker-lab/sirius] Custom-database CLI (Issue #106)

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Hello! I am having the same (or similar) issue with the 5.8.3 version:

java.lang.NullPointerException: Name is null at java.base/java.lang.Enum.valueOf(Unknown Source) at de.unijena.bioinf.storage.blob.Compressible$Compression.valueOf(Compressible.java:44) at de.unijena.bioinf.storage.blob.CompressibleBlobStorage.of(CompressibleBlobStorage.java:40) at de.unijena.bioinf.chemdb.custom.CustomDatabase.open(CustomDatabase.java:99) at de.unijena.bioinf.chemdb.SearchableDatabases.loadCustomDatabaseFromLocation(SearchableDatabases.java:195) at de.unijena.bioinf.ms.gui.fingerid.custom_db.DatabaseDialog$ImportDatabaseDialog.lambda$runImportJob$2(DatabaseDialog.java:349) at de.unijena.bioinf.jjobs.LoadingBackroundTask$1.compute(LoadingBackroundTask.java:35) at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source)

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YasinEl commented 3 days ago

Hello SIRIUS scientists :)

in SIRIUS 6.0.0 under Windows 11 I am still running into the same problem (see below). Also I think the documentation should be updated regarding arguments (--location instead of --output).

Thanks!

sirius custom-db -i structures.tsv --name tmp_sirius_db --location output\

java.lang.NullPointerException: Name is null
    at java.base/java.lang.Enum.valueOf(Unknown Source)
    at de.unijena.bioinf.storage.blob.Compressible$Compression.valueOf(Compressible.java:44)
    at de.unijena.bioinf.storage.blob.CompressibleBlobStorage.of(CompressibleBlobStorage.java:40)
    at de.unijena.bioinf.chemdb.custom.CustomDatabases.open(CustomDatabases.java:191)
    at de.unijena.bioinf.chemdb.custom.CustomDatabases.createOrOpen(CustomDatabases.java:207)
    at de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow.compute(CustomDBOptions.java:188)
    at de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions$CustomDBWorkflow.compute(CustomDBOptions.java:144)
    at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:124)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)