As of SIRIUS 4.7 I get all kinds of exceptions when trying to run on Windows, both on my laptop and on AppVeyor
C:\Users\rick\Documents\Rproj\sirius>sirius -i C:\Users\rick\Documents\Rproj\sirius-demo-data\ms\Bicuculline.ms -o C:\Users\rick\Documents\Rproj\sirius-demo-data\out formula
INFO 08:56:54 - Sirius Workspace Successfull initialized at: C:\Users\rick\.sirius-4.7
INFO 08:56:54 - You run SIRIUS 4.7.3
INFO 08:56:54 - Sirius was compiled with the following ILP solvers: GLPK-v1.7.0 (included), Gurobi-v9.1.1, CPLEX-v12.7.1, COIN-OR-v1.17.3
INFO 08:56:54 - Treebuilder priorities loaded from 'sirius.properties' are: [GUROBI, CPLEX, CLP, GLPK]
INFO 08:56:54 - CPU check done. 8 cores that handle 16 threads were found.
INFO 08:56:54 - Bug reporter initialized.
INFO 08:56:54 - Web API initialized.
INFO 08:56:55 - Running with following arguments: [-i, C:\Users\rick\Documents\Rproj\sirius-demo-data\ms\Bicuculline.ms, -o, C:\Users\rick\Documents\Rproj\sirius-demo-data\out, formula]
INFO 08:56:55 - Job manager successful initialized with 8 CPU thread(s) and 3 IO thread(s).
FINE 08:56:55 - <0>[InputExpanderJJob] Running post processing
FINE 08:56:55 - <0>[InputExpanderJJob] Running cleanup
INFO 08:56:55 - <1>[InputExpanderJJob] Expanding Input Files: 'C:\Users\rick\Documents\Rproj\sirius-demo-data\ms\Bicuculline.ms'...
INFO 08:56:55 - <1>[InputExpanderJJob] ...Input Files successfully expanded!
FINE 08:56:55 - <1>[InputExpanderJJob] Running post processing
FINE 08:56:55 - <1>[InputExpanderJJob] Running cleanup
WARNING 08:56:56 - 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-v1.17.3: gurobi/GRBException
WARNING 08:56:56 - 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-v1.17.3: gurobi/GRBException
WARNING 08:56:56 - 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-v1.17.3: gurobi/GRBException
WARNING 08:56:56 - 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-v1.17.3: ilog/concert/IloNumVar
WARNING 08:56:56 - 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-v1.17.3: ilog/concert/IloNumVar
WARNING 08:56:56 - 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-v1.17.3: ilog/concert/IloNumVar
WARNING 08:56:56 - Could not load Solver 'CLP': java.lang.UnsatisfiedLinkError: C:\Users\rick\Documents\Rproj\sirius\CLPModelWrapper_JNI.dll: Kan opgegeven procedure niet vinden
WARNING 08:56:56 - Could not load Solver 'CLP': java.lang.NoClassDefFoundError: Could not initialize class de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.CLPModel_JNI
WARNING 08:56:56 - Could not load Solver 'CLP': java.lang.NoClassDefFoundError: Could not initialize class de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.CLPModel_JNI
WARNING 08:56:56 - Could not find and load de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.GLPKSolver! Sirius was compiled with the following ILP solvers: GLPK-v1.7.0 (included), Gurobi-v9.1.1, CPLEX-v12.7.1, COIN-OR-v1.17.3: de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.GLPKSolver
WARNING 08:56:56 - Could not find and load de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.GLPKSolver! Sirius was compiled with the following ILP solvers: GLPK-v1.7.0 (included), Gurobi-v9.1.1, CPLEX-v12.7.1, COIN-OR-v1.17.3: de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.GLPKSolver
WARNING 08:56:56 - Could not find and load de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.GLPKSolver! Sirius was compiled with the following ILP solvers: GLPK-v1.7.0 (included), Gurobi-v9.1.1, CPLEX-v12.7.1, COIN-OR-v1.17.3: de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.ilp.GLPKSolver
SEVERE 08:56:56 - Your system does not ship with any instantiatable ILP solver. Please install either CLP, Gurobi or CPLEX to use SIRIUS.
SEVERE 08:56:56 - Your system does not ship with any instantiatable ILP solver. Please install either CLP, Gurobi or CPLEX to use SIRIUS.
SEVERE 08:56:56 - Your system does not ship with any instantiatable ILP solver. Please install either CLP, Gurobi or CPLEX to use SIRIUS.
SEVERE 08:56:56 - <28>[RecalibrationJob] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <27>[RecalibrationJob] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <26>[RecalibrationJob] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <17>[FasterTreeComputationInstance] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <18>[FasterTreeComputationInstance] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <19>[FasterTreeComputationInstance] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <16>[SiriusIdentificationJob] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <14>[SiriusIdentificationJob] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <15>[SiriusIdentificationJob] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <13>[SiriusSubToolJob | 1_Bicuculline_Bicuculline@368m/z] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <10>[SiriusSubToolJob | 0_Bicuculline_Bicuculline@368m/z] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <7>[SiriusSubToolJob | 2_Bicuculline_Bicuculline@368m/z] Failed!
java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance.recalibrate(FasterTreeComputationInstance.java:557)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:532)
at de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance$RecalibrationJob.compute(FasterTreeComputationInstance.java:518)
at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:120)
at de.unijena.bioinf.jjobs.BasicMasterJJob$1.compute(BasicMasterJJob.java:87)
at java.base/java.util.concurrent.RecursiveTask.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$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)
SEVERE 08:56:56 - <7>[SiriusSubToolJob | 2_Bicuculline_Bicuculline@368m/z] ToolChain Job failed due to: java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
SEVERE 08:56:56 - <10>[SiriusSubToolJob | 0_Bicuculline_Bicuculline@368m/z] ToolChain Job failed due to: java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
SEVERE 08:56:56 - <13>[SiriusSubToolJob | 1_Bicuculline_Bicuculline@368m/z] ToolChain Job failed due to: java.lang.NullPointerException: Cannot invoke "de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder.computeTree()" because "finalBuilder" is null
INFO 08:56:56 - Workflow has been finished!
INFO 08:56:56 - Executing Postprocessing...
INFO 08:56:56 - Writing summary files...
INFO 08:56:56 - Project-Space summaries successfully written!
INFO 08:56:56 - CLI shut down hook: SIRIUS is cleaning up threads and shuts down...
Please cite the following publications when using our tool:
When using the SIRIUS Software please cite the following paper:
Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Alexander A. Aksenov, Alexey V. Melnik, Marvin Meusel, Pieter C. Dorrestein, Juho Rousu and Sebastian Böcker
SIRIUS4: a rapid tool for turning tandem mass spectra into metabolite structure information
Nat Methods, 16, 2019. https://doi.org/10.1038/s41592-019-0344-8
Depending on the tools you have used please also cite:
Kai Dührkop, Louis-Félix Nothias, Markus Fleischauer, Raphael Reher, Marcus Ludwig, Martin A. Hoffmann, Daniel Petras, William H. Gerwick, Juho Rousu, Pieter C. Dorrestein and Sebastian Böcker
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
Nature Biotechnology, 2020. https://doi.org/10.1038/s41587-020-0740-8
(Cite if you are using: CANOPUS)
Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David S. Wishart
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy
J Cheminf, 8, 2016. https://doi.org/10.1186/s13321-016-0174-y
(Cite if you are using: CANOPUS)
Kai Dührkop, Huibin Shen, Marvin Meusel, Juho Rousu and Sebastian Böcker
Searching molecular structure databases with tandem mass spectra using CSI:FingerID
Proc Natl Acad Sci U S A, 112, 2015. https://doi.org/10.1073/pnas.1509788112
(Cite if you are using: CSI:FingerID)
Sebastian Böcker and Kai Dührkop
Fragmentation trees reloaded
J Cheminform, 8, 2016. https://doi.org/10.1186/s13321-016-0116-8
(Cite if you are using: Fragmentation Trees)
Sebastian Böcker, Matthias Letzel, Zsuzsanna Lipták and Anton Pervukhin
SIRIUS: Decomposing isotope patterns for metabolite identification
Bioinformatics, 25, 2009. https://doi.org/10.1093/bioinformatics/btn603
(Cite if you are using: Isotope Pattern analysis)
Marcus Ludwig, Louis-Félix Nothias, Kai Dührkop, Irina Koester, Markus Fleischauer, Martin A. Hoffmann, Daniel Petras, Fernando Vargas, Mustafa Morsy, Lihini Aluwihare, Pieter C. Dorrestein, Sebastian Böcker
ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules
bioRxiv, 2019. https://doi.org/10.1101/842740
(Cite if you are using: ZODIAC)