BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
SYS_ERROR:org.xml.sax.SAXException: value for 'proportionOfThickness' attribute in featureRange element must be between 0 and 1 in null at line 1192 column 147 #16
Rendering CGVIEW image...
java -Xmx1500m -jar cgview/cgview.jar -f jpg -i /Data/NGS_1165_Circos_genomes/genome/scratch/Bacillus_paralicheniformis.fna.xml -o /Data/NGS_1165_Circos_genomes/genome/Bacillus_paralicheniformis.fna.jpg
Parsing XML input.
SYS_ERROR:org.xml.sax.SAXException: value for 'proportionOfThickness' attribute in featureRange element must be between 0 and 1 in null at line 1192 column 147
SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.handleFeatureRange(CgviewFactory.java:2215)
SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.startElement(CgviewFactory.java:516)
SYS_ERROR: at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
SYS_ERROR: at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source)
SYS_ERROR: at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
SYS_ERROR: at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
SYS_ERROR: at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
SYS_ERROR: at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
SYS_ERROR: at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
SYS_ERROR: at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
SYS_ERROR: at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.createCgviewFromFile(CgviewFactory.java:300)
SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewIO.main(CgviewIO.java:1056)
SYS_ERROR:The following error occurred: org.xml.sax.SAXException: value for 'proportionOfThickness' attribute in featureRange element must be between 0 and 1 in null at line 1192 column 147
Done.
This is what I'm getting while plotting circular plot.
Need help
Your query File: /Data/NGS_1165_Circos_genomes/genome/Bacillus_paralicheniformis.fna
Multi-FASTA detected, Rewriting headers
Initializing XML output..
Running BLAST... Sequence length: 3976743 Spaced1Bacillus_paralicheniformis.fna.nin exists, skipping .. Bacillus_paralicheni... exists, skipping .. Spaced1Bacillus_paralicheniformis.fna.nin exists, skipping .. Bacillus_paralicheni... exists, skipping .. Spaced1Bacillus_paralicheniformis.fna.nin exists, skipping .. G1_gene.fnaVsSpaced1... exists, skipping .. Spaced1Bacillus_paralicheniformis.fna.nin exists, skipping .. Bacillus_licheniform... exists, skipping .. Spaced1Bacillus_paralicheniformis.fna.nin exists, skipping .. Bacillus_amyloliquef... exists, skipping ..
Parsing BLAST Results...
Rendering CGVIEW image... java -Xmx1500m -jar cgview/cgview.jar -f jpg -i /Data/NGS_1165_Circos_genomes/genome/scratch/Bacillus_paralicheniformis.fna.xml -o /Data/NGS_1165_Circos_genomes/genome/Bacillus_paralicheniformis.fna.jpg Parsing XML input. SYS_ERROR:org.xml.sax.SAXException: value for 'proportionOfThickness' attribute in featureRange element must be between 0 and 1 in null at line 1192 column 147 SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.handleFeatureRange(CgviewFactory.java:2215) SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.startElement(CgviewFactory.java:516) SYS_ERROR: at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) SYS_ERROR: at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) SYS_ERROR: at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) SYS_ERROR: at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) SYS_ERROR: at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) SYS_ERROR: at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) SYS_ERROR: at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source) SYS_ERROR: at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) SYS_ERROR: at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.createCgviewFromFile(CgviewFactory.java:300) SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewIO.main(CgviewIO.java:1056) SYS_ERROR:The following error occurred: org.xml.sax.SAXException: value for 'proportionOfThickness' attribute in featureRange element must be between 0 and 1 in null at line 1192 column 147 Done.
This is what I'm getting while plotting circular plot. Need help