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)
May 25, 2024 11:31:12 PM de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilderFactory getTreeBuilder
WARNING: Could not load Solver 'CLP': java.lang.NoClassDefFoundError: Could not initialize class de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.CLPModel_JNI
May 25, 2024 11:31:12 PM de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilderFactory getTreeBuilderFromClass
WARNING: Could not load GrbSolver! Sirius was compiled with the following ILP solvers: GLPK-v1.7.0 (included), Gurobi-v9.1.1, CPLEX-v12.7.1, COIN-OR-v2.10.8.4: Could not initialize class de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.GrbSolver
May 25, 2024 11:31:12 PM de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilderFactory getTreeBuilderFromClass
WARNING: Could not load CPLEXSolver! Sirius was compiled with the following ILP solvers: GLPK-v1.7.0 (included), Gurobi-v9.1.1, CPLEX-v12.7.1, COIN-OR-v2.10.8.4: ilog/concert/IloNumVar
May 25, 2024 11:31:12 PM de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilderFactory getTreeBuilder
SEVERE: Your system does not ship with any instantiatable ILP solver. Please install either CLP, Gurobi or CPLEX to use SIRIUS.
May 25, 2024 11:31:12 PM de.unijena.bioinf.jjobs.JJob lambda$logError$2
SEVERE: <543>[TreeComputationJob-543 | 6-Ethoxy-2-mercaptobenzothiazole@212.0198m/z | C9H9NOS2 + H+ (5.045)] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "this.treeBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$TreeComputationJob.compute(FasterTreeComputationInstance.java:492)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$TreeComputationJob.compute(FasterTreeComputationInstance.java:474)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117)
at de.unijena.bioinf.jjobs.BatchJJob.compute(BatchJJob.java:28)
at de.unijena.bioinf.jjobs.BatchJJob.compute(BatchJJob.java:10)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:101)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.awaitDone(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.join(Unknown Source)
at de.unijena.bioinf.jjobs.BasicJJob.awaitResult(BasicJJob.java:211)
at de.unijena.bioinf.jjobs.JJob.takeResult(JJob.java:249)
at java.base/java.util.ArrayList.forEach(Unknown Source)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.estimateTreeSizeAndRecalibration(FasterTreeComputationInstance.java:242)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.compute(FasterTreeComputationInstance.java:173)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.compute(FasterTreeComputationInstance.java:55)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:101)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.awaitDone(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.join(Unknown Source)
at de.unijena.bioinf.jjobs.BasicJJob.awaitResult(BasicJJob.java:211)
at de.unijena.bioinf.sirius.Sirius$SiriusIdentificationJob.compute(Sirius.java:640)
at de.unijena.bioinf.sirius.Sirius$SiriusIdentificationJob.compute(Sirius.java:623)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117)
at java.base/java.util.concurrent.ForkJoinTask$AdaptedCallable.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool.scan(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool.runWorker(Unknown Source)
at java.base/java.util.concurrent.ForkJoinWorkerThread.run(Unknown Source)
May 25, 2024 11:31:12 PM de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilderFactory getTreeBuilder WARNING: Could not load Solver 'CLP': java.lang.NoClassDefFoundError: Could not initialize class de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.CLPModel_JNI May 25, 2024 11:31:12 PM de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilderFactory getTreeBuilderFromClass WARNING: Could not load GrbSolver! Sirius was compiled with the following ILP solvers: GLPK-v1.7.0 (included), Gurobi-v9.1.1, CPLEX-v12.7.1, COIN-OR-v2.10.8.4: Could not initialize class de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.GrbSolver May 25, 2024 11:31:12 PM de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilderFactory getTreeBuilderFromClass WARNING: Could not load CPLEXSolver! Sirius was compiled with the following ILP solvers: GLPK-v1.7.0 (included), Gurobi-v9.1.1, CPLEX-v12.7.1, COIN-OR-v2.10.8.4: ilog/concert/IloNumVar May 25, 2024 11:31:12 PM de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilderFactory getTreeBuilder SEVERE: Your system does not ship with any instantiatable ILP solver. Please install either CLP, Gurobi or CPLEX to use SIRIUS. May 25, 2024 11:31:12 PM de.unijena.bioinf.jjobs.JJob lambda$logError$2 SEVERE: <543>[TreeComputationJob-543 | 6-Ethoxy-2-mercaptobenzothiazole@212.0198m/z | C9H9NOS2 + H+ (5.045)] Failed! java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "this.treeBuilder" is null at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$TreeComputationJob.compute(FasterTreeComputationInstance.java:492) at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$TreeComputationJob.compute(FasterTreeComputationInstance.java:474) at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117) at de.unijena.bioinf.jjobs.BatchJJob.compute(BatchJJob.java:28) at de.unijena.bioinf.jjobs.BatchJJob.compute(BatchJJob.java:10) at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117) at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:101) at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source) at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source) at java.base/java.util.concurrent.ForkJoinTask.awaitDone(Unknown Source) at java.base/java.util.concurrent.ForkJoinTask.join(Unknown Source) at de.unijena.bioinf.jjobs.BasicJJob.awaitResult(BasicJJob.java:211) at de.unijena.bioinf.jjobs.JJob.takeResult(JJob.java:249) at java.base/java.util.ArrayList.forEach(Unknown Source) at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.estimateTreeSizeAndRecalibration(FasterTreeComputationInstance.java:242) at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.compute(FasterTreeComputationInstance.java:173) at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.compute(FasterTreeComputationInstance.java:55) at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117) at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:101) at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source) at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source) at java.base/java.util.concurrent.ForkJoinTask.awaitDone(Unknown Source) at java.base/java.util.concurrent.ForkJoinTask.join(Unknown Source) at de.unijena.bioinf.jjobs.BasicJJob.awaitResult(BasicJJob.java:211) at de.unijena.bioinf.sirius.Sirius$SiriusIdentificationJob.compute(Sirius.java:640) at de.unijena.bioinf.sirius.Sirius$SiriusIdentificationJob.compute(Sirius.java:623) at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117) at java.base/java.util.concurrent.ForkJoinTask$AdaptedCallable.exec(Unknown Source) at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source) at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(Unknown Source) at java.base/java.util.concurrent.ForkJoinPool.scan(Unknown Source) at java.base/java.util.concurrent.ForkJoinPool.runWorker(Unknown Source) at java.base/java.util.concurrent.ForkJoinWorkerThread.run(Unknown Source)