************************************************************************** *** Welcome to KNIME v2.6.1.0034748 - the Konstanz Information Miner *** *** Copyright, 2003 - 2012, Uni Konstanz and KNIME GmbH, Germany *** ************************************************************************** Log file is located at: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/.metadata/knime/knime.log WARN SingleNodeContainerPersistorVersion200 Substituted 'org.knime.knip.imagej1.io.IJImageReaderNodeFactory' for unknown factory 'org.knime.knip.base.nodes.io.ijimagereader.IJImageReaderNodeFactory' WARN SingleNodeContainerPersistorVersion200 Substituted 'org.knime.knip.base.nodes.proc.ProjectorNodeFactory' for unknown factory 'org.knime.knip.base.nodes.proc.projector.ProjectorNodeFactory' ERROR WorkflowPersistorVersion200 Unable to load node with ID suffix 3 into workflow, skipping it: null WARN SingleNodeContainerPersistorVersion200 Substituted 'org.knime.knip.base.nodes.proc.ProjectorNodeFactory' for unknown factory 'org.knime.knip.base.nodes.proc.projector.ProjectorNodeFactory' ERROR WorkflowPersistorVersion200 Unable to load node with ID suffix 548 into workflow, skipping it: null WARN SingleNodeContainerPersistorVersion200 Substituted 'org.knime.knip.base.nodes.proc.ThresholderNodeFactory' for unknown factory 'org.knime.knip.base.nodes.proc.thresholder.ThresholderNodeFactory' ERROR WorkflowPersistorVersion200 Unable to load node with ID suffix 4 into workflow, skipping it: null WARN SingleNodeContainerPersistorVersion200 Substituted 'org.knime.knip.base.nodes.seg.ConnectedCompAnalysisNodeFactory' for unknown factory 'org.knime.knip.base.nodes.seg.cca.ConnectedCompAnalysisNodeFactory' ERROR WorkflowPersistorVersion200 Unable to load node with ID suffix 154 into workflow, skipping it: null ERROR Segment Features Loading model settings failed: ConfigBase for key "segment_feature_set" not found. ERROR Segment Features Loading model settings failed: ConfigBase for key "segment_feature_set" not found. ERROR Segment Overlay Viewer Loading model settings failed: String for key "cfg_img_col" not found. ERROR Segment Overlay Viewer Loading model settings failed: String for key "cfg_img_col" not found. ERROR Segment Overlay Viewer Loading model settings failed: String for key "cfg_img_col" not found. ERROR Segment Overlay Viewer Loading model settings failed: String for key "cfg_img_col" not found. WARN SingleNodeContainerPersistorVersion200 Substituted 'org.knime.knip.base.nodes.seg.ConnectedCompAnalysisNodeFactory' for unknown factory 'org.knime.knip.base.nodes.seg.cca.ConnectedCompAnalysisNodeFactory' ERROR WorkflowPersistorVersion200 Unable to load node with ID suffix 116 into workflow, skipping it: null ERROR Segment Features Loading model settings failed: ConfigBase for key "segment_feature_set" not found. ERROR Segment Overlay Viewer Loading model settings failed: String for key "cfg_img_col" not found. ERROR Segment Overlay Viewer Loading model settings failed: String for key "cfg_img_col" not found. WARN XLS Reader The file '/Applications/knime/knime.app/Contents/MacOS/C:\Users\M.Yosry\Desktop\Heidelberg\Thesis Project\Mat_a_obs_v5.0.xls' can't be accessed anymore! WARN XLS Reader Specified file doesn't exist (/Applications/knime/knime.app/Contents/MacOS/C:\Users\M.Yosry\Desktop\Heidelberg\Thesis Project\Mat_a_obs_v5.0.xls) ERROR LoadWorkflowRunnable Errors during load: Status: DataLoadError: Spots-Finder_modd_all QC_adjust usee 0 loaded with error during data load ERROR LoadWorkflowRunnable Status: DataLoadError: Spots-Finder_modd_all QC_adjust usee 0 ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.seg.table2lab.Table2LabelingNodeFactory" ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.seg.table2lab.Table2LabelingNodeFactory" ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.misc.ij.IJSnippetNodeFactory" ERROR LoadWorkflowRunnable Status: Error: Preprocessing 0:274 ERROR LoadWorkflowRunnable Status: Error: Unable to load node with ID suffix 3 into workflow, skipping it: null ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.misc.ij.IJSnippetNodeFactory" ERROR LoadWorkflowRunnable Status: Error: Unable to load node with ID suffix 548 into workflow, skipping it: null ERROR LoadWorkflowRunnable Status: Warning: Joiner 0:274:549 ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Error: Segmentaion :: Nuclei :: Cells 0:277 ERROR LoadWorkflowRunnable Status: Error: Segment :: Nulcei :: QC 0:277:535 ERROR LoadWorkflowRunnable Status: Error: Unable to load node with ID suffix 4 into workflow, skipping it: null ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.proc.binary.ops.BinaryOpsNodeFactory" ERROR LoadWorkflowRunnable Status: Error: Unable to load node with ID suffix 154 into workflow, skipping it: null ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.misc.ij.IJSnippetNodeFactory" ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.seg.table2lab.Table2LabelingNodeFactory" ERROR LoadWorkflowRunnable Status: Error: Segment Features 0:277:535:168 ERROR LoadWorkflowRunnable Status: Error: Loading model settings failed: ConfigBase for key "segment_feature_set" not found. ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Error: Segment :: Cells :: QC 0:277:540 ERROR LoadWorkflowRunnable Status: Error: Segment Features 0:277:540:168 ERROR LoadWorkflowRunnable Status: Error: Loading model settings failed: ConfigBase for key "segment_feature_set" not found. ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Error: Segment Overlay Viewer 0:277:533 ERROR LoadWorkflowRunnable Status: Error: Loading model settings failed: String for key "cfg_img_col" not found. ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Error: Segment Overlay Viewer 0:277:273 ERROR LoadWorkflowRunnable Status: Error: Loading model settings failed: String for key "cfg_img_col" not found. ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Error: To visualize / to Adjust 0:277:542 ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.seg.table2lab.Table2LabelingNodeFactory" ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.seg.table2lab.Table2LabelingNodeFactory" ERROR LoadWorkflowRunnable Status: Warning: Joiner 0:277:542:530 ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Error: Segment Overlay Viewer 0:277:539 ERROR LoadWorkflowRunnable Status: Error: Loading model settings failed: String for key "cfg_img_col" not found. ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Error: Segment Overlay Viewer 0:277:531 ERROR LoadWorkflowRunnable Status: Error: Loading model settings failed: String for key "cfg_img_col" not found. ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Error: Segmentation :: Spots 0:112 ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.misc.ij.IJSnippetNodeFactory" ERROR LoadWorkflowRunnable Status: Error: Unable to load node with ID suffix 116 into workflow, skipping it: null ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.misc.ij.IJSnippetNodeFactory" ERROR LoadWorkflowRunnable Status: Error: Unable to load factory class "org.knime.knip.base.nodes.seg.table2lab.Table2LabelingNodeFactory" ERROR LoadWorkflowRunnable Status: Error: Segment Features 0:112:168 ERROR LoadWorkflowRunnable Status: Error: Loading model settings failed: ConfigBase for key "segment_feature_set" not found. ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Warning: Joiner 0:112:452 ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Warning: Joiner 0:112:527 ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: Error: Segment Overlay Viewer 0:112:278 ERROR LoadWorkflowRunnable Status: Error: Loading model settings failed: String for key "cfg_img_col" not found. ERROR LoadWorkflowRunnable Status: Error: Segment Overlay Viewer 0:112:528 ERROR LoadWorkflowRunnable Status: Error: Loading model settings failed: String for key "cfg_img_col" not found. ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: DataLoadError: Statistics :: Cells 0:523 ERROR LoadWorkflowRunnable Status: DataLoadError: Table Creator 0:523:9 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Table Creator": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Statistics __ Cells (#523)/Table Creator (#9)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to CONFIGURED ERROR LoadWorkflowRunnable Status: DataLoadError: Statistics :: Cells with Spots :: Nuclei with Spots 0:529 ERROR LoadWorkflowRunnable Status: DataLoadError: Statistics_No. Spots per cell 0:529:538 ERROR LoadWorkflowRunnable Status: DataLoadError: Concatenate 0:529:538:310 ERROR LoadWorkflowRunnable Status: DataLoadError: Table Creator 0:529:538:310:57 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Table Creator": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Statistics __ Cells with Spots __ Nuclei with Spots (#529)/Statistics (#538)/Concatenate (#310)/Table Creator (#57)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to CONFIGURED ERROR LoadWorkflowRunnable Status: DataLoadError: No. of cells showing certain number of spots 0:529:542 ERROR LoadWorkflowRunnable Status: DataLoadError: Concatenate 0:529:542:211 ERROR LoadWorkflowRunnable Status: DataLoadError: Table Creator 0:529:542:211:9 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Table Creator": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Statistics __ Cells with Spots __ Nuclei with Spots (#529)/No_ of cells showing certain number of spots (#542)/Concatenate (#211)/Table Creator (#9)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to CONFIGURED ERROR LoadWorkflowRunnable Status: DataLoadError: Table Creator 0:529:542:211:203 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Table Creator": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Statistics __ Cells with Spots __ Nuclei with Spots (#529)/No_ of cells showing certain number of spots (#542)/Concatenate (#211)/Table Creator (#203)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to CONFIGURED ERROR LoadWorkflowRunnable Status: DataLoadError: Concatenate 0:529:542:496 ERROR LoadWorkflowRunnable Status: DataLoadError: Table Creator 0:529:542:496:9 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Table Creator": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Statistics __ Cells with Spots __ Nuclei with Spots (#529)/No_ of cells showing certain number of spots (#542)/Concatenate (#496)/Table Creator (#9)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to CONFIGURED ERROR LoadWorkflowRunnable Status: DataLoadError: Table Creator 0:529:542:496:203 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Table Creator": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Statistics __ Cells with Spots __ Nuclei with Spots (#529)/No_ of cells showing certain number of spots (#542)/Concatenate (#496)/Table Creator (#203)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to CONFIGURED ERROR LoadWorkflowRunnable Status: DataLoadError: No. of nuclei showing certain number of spots 0:529:541 ERROR LoadWorkflowRunnable Status: DataLoadError: Concatenate 0:529:541:501 ERROR LoadWorkflowRunnable Status: DataLoadError: Table Creator 0:529:541:501:9 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Table Creator": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Statistics __ Cells with Spots __ Nuclei with Spots (#529)/No_ of nuclei showing certain number of spots (#541)/Concatenate (#501)/Table Creator (#9)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to CONFIGURED ERROR LoadWorkflowRunnable Status: DataLoadError: Table Creator 0:529:541:501:203 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Table Creator": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Statistics __ Cells with Spots __ Nuclei with Spots (#529)/No_ of nuclei showing certain number of spots (#541)/Concatenate (#501)/Table Creator (#203)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to CONFIGURED ERROR LoadWorkflowRunnable Status: DataLoadError: Concatenate 0:529:541:532 ERROR LoadWorkflowRunnable Status: DataLoadError: Table Creator 0:529:541:532:9 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Table Creator": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Statistics __ Cells with Spots __ Nuclei with Spots (#529)/No_ of nuclei showing certain number of spots (#541)/Concatenate (#532)/Table Creator (#9)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to CONFIGURED ERROR LoadWorkflowRunnable Status: DataLoadError: Table Creator 0:529:541:532:203 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Table Creator": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Statistics __ Cells with Spots __ Nuclei with Spots (#529)/No_ of nuclei showing certain number of spots (#541)/Concatenate (#532)/Table Creator (#203)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to CONFIGURED ERROR LoadWorkflowRunnable Status: Error: Postprocessing :: Nuclei :: Cells 0:519 ERROR LoadWorkflowRunnable Status: Error: Some node states were invalid ERROR LoadWorkflowRunnable Status: Error: Postprocessing :: Spots 0:358 ERROR LoadWorkflowRunnable Status: Error: Some node states were invalid ERROR LoadWorkflowRunnable Status: Warning: State has changed from CONFIGURED to IDLE ERROR LoadWorkflowRunnable Status: DataLoadError: Concatenate 0:310 ERROR LoadWorkflowRunnable Status: DataLoadError: Table Creator 0:310:57 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Table Creator": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Concatenate (#310)/Table Creator (#57)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to CONFIGURED ERROR LoadWorkflowRunnable Status: DataLoadError: Matching to the library ver2 0:545 ERROR LoadWorkflowRunnable Status: DataLoadError: Extracting info from library 0:545:581 ERROR LoadWorkflowRunnable Status: DataLoadError: XLS Reader 0:545:581:533 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "XLS Reader": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Matching to the library ver2 (#545)/Extracting info from library (#581)/XLS Reader (#533)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: State has changed from EXECUTED to IDLE ERROR LoadWorkflowRunnable Status: DataLoadError: Java Snippet (simple) 0:545:581:566 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Java Snippet (simple)": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Matching to the library ver2 (#545)/Extracting info from library (#581)/Java Snippet (#566)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: Row Filter 0:545:581:557 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Row Filter": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Matching to the library ver2 (#545)/Extracting info from library (#581)/Row Filter (#557)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: Row Filter 0:545:581:60 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Row Filter": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Matching to the library ver2 (#545)/Extracting info from library (#581)/Row Filter (#60)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: Row Filter 0:545:581:555 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Row Filter": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Matching to the library ver2 (#545)/Extracting info from library (#581)/Row Filter (#555)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: Row Filter 0:545:581:556 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "Row Filter": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Matching to the library ver2 (#545)/Extracting info from library (#581)/Row Filter (#556)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: RowID (deprecated) 0:545:581:576 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "RowID (deprecated)": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Matching to the library ver2 (#545)/Extracting info from library (#581)/RowID (#576)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: RowID (deprecated) 0:545:581:567 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "RowID (deprecated)": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Matching to the library ver2 (#545)/Extracting info from library (#581)/RowID (#567)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: RowID (deprecated) 0:545:581:578 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "RowID (deprecated)": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Matching to the library ver2 (#545)/Extracting info from library (#581)/RowID (#578)/port_1/data.xml ERROR LoadWorkflowRunnable Status: DataLoadError: RowID (deprecated) 0:545:581:577 ERROR LoadWorkflowRunnable Status: DataLoadError: Unable to load port content for node "RowID (deprecated)": No such data file: /Users/Stephi/Documents/Daten Promotion/Microscopy/KNIME_WS/Spots-Finder_modd_all QC_adjust usee/Matching to the library ver2 (#545)/Extracting info from library (#581)/RowID (#577)/port_1/data.xml