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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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sirius-network-connection #144

Closed xdkong closed 6 months ago

xdkong commented 7 months ago

Dear developers, When I use SIRIUS, the command is as follows: /data/software/sirius-5.8.5/sirius/bin/sirius --maxmz=850 --cores 20 -i /data/kong/soybean/metabolome/mzmine_sirius.mgf -o /data/kong/soybean/metabolome/sirius_altissues11302023 formula -c 50 -p qtof -d BIO However, I encountered some problems, as follows: Nov 30, 2023 4:04:45 PM de.unijena.bioinf.jjobs.JJob lambda$logError$2 SEVERE: <2869>[SiriusSubToolJob-2869 | 252_mzmine_sirius_657@785m/z] Failed! java.lang.NullPointerException: Service URL is null. This might be caused by a missing login. at de.unijena.bioinf.ms.rest.client.AbstractCsiClient.getBaseURI(AbstractCsiClient.java:82) at de.unijena.bioinf.ms.rest.client.AbstractCsiClient.buildWebapiURI(AbstractCsiClient.java:72) at de.unijena.bioinf.ms.rest.client.AbstractCsiClient.buildVersionSpecificWebapiURI(AbstractCsiClient.java:76) at de.unijena.bioinf.ms.rest.client.chemdb.StructureSearchClient.lambda$getFormulas$1(StructureSearchClient.java:91) at de.unijena.bioinf.ms.rest.client.AbstractClient.execute(AbstractClient.java:133) at de.unijena.bioinf.ms.rest.client.chemdb.StructureSearchClient.getFormulas(StructureSearchClient.java:90) at de.unijena.bioinf.chemdb.RESTDatabase.lookupMolecularFormulas(RESTDatabase.java:122) at de.unijena.bioinf.chemdb.WebWithCustomDatabase.lambda$loadMolecularFormulas$1(WebWithCustomDatabase.java:122) at de.unijena.bioinf.webapi.rest.RestAPI.lambda$consumeStructureDB$19(RestAPI.java:353) at de.unijena.bioinf.rest.ProxyManager.consumeClient(ProxyManager.java:439) at de.unijena.bioinf.rest.ProxyManager.consumeClient(ProxyManager.java:432) at de.unijena.bioinf.webapi.rest.RestAPI.consumeStructureDB(RestAPI.java:351) at de.unijena.bioinf.chemdb.WebWithCustomDatabase.loadMolecularFormulas(WebWithCustomDatabase.java:121) at de.unijena.bioinf.chemdb.WebWithCustomDatabase.loadMolecularFormulas(WebWithCustomDatabase.java:106) at de.unijena.bioinf.fingerid.FormulaWhiteListJob.lambda$compute$1(FormulaWhiteListJob.java:81) at de.unijena.bioinf.rest.NetUtils.tryAndWait(NetUtils.java:93) at de.unijena.bioinf.rest.NetUtils.tryAndWait(NetUtils.java:85) at de.unijena.bioinf.fingerid.FormulaWhiteListJob.compute(FormulaWhiteListJob.java:80) at de.unijena.bioinf.fingerid.FormulaWhiteListJob.compute(FormulaWhiteListJob.java:44) at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) The above is the command line I used in Linux. Also, I used the GUI version in the Windows system and encountered network connection issues： 屏幕截图 2023-11-30 161144

Best, Xiangdong

joXemMx commented 6 months ago

Hi, it may be that your issue is simply caused by not being logged in correctly (see java.lang.NullPointerException: Service URL is null. This might be caused by a missing login). Please see if this was the problem.