BRIG error message

[Bicalho]

Hi There,

I am getting the following error message from BRIG when trying to run a simple genome comparison with 4 bacterial genomes.

Rendering CGVIEW image...
java -Xmx1000m -jar cgview\cgview.jar -f jpg -i I:\TPcomparison\scratch\TP6375.fasta.xml -o I:\TPcomparison\TP6375.fasta.jpg
Parsing XML input.
SYS_ERRORrg.xml.sax.SAXException: value for 'sequenceLength' attribute in cgview element must be less than 20000000 in null at line 1 column 1050
SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.handleCgview(CgviewFactory.java:593)
SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.startElement(CgviewFactory.java:510)
SYS_ERROR: at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
SYS_ERROR: at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
SYS_ERROR: at org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source)
SYS_ERROR: at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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 'sequenceLength' attribute in cgview element must be less than 20000000 in null at line 1 column 1050
Done.

any help?

[IanWilson]

Hi Bicalho,

I've just tried running BRIG myself and come up against the same problem. I'm not 100% sure but my guess would be that at least one of your genomes is larger than 20Mb. Is that the case?
It might be worth just looking at CDS features rather than entire genomes.

Best of luck!

[himani]

Hi
I am also getting same problem.

SYS_ERRORrg.xml.sax.SAXException: value for 'sequenceLength' attribute in cgview element must be less than 20000000 in null at line 1 column 1061
SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.handleCgview(CgviewFactory.java:593)
SYS_ERROR: at ca.ualberta.stothard.cgview.CgviewFactory.startElement(CgviewFactory.java:510)
SYS_ERROR: at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
SYS_ERROR: at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
SYS_ERROR: at org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source)
SYS_ERROR: at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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.XML11Configuration.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 'sequenceLength' attribute in cgview element must be less than 20000000 in null at line 1 column 1061


Please inform me if there is any size limitation preoblem in BRIG?,as my genome size is 200 MB.


Thanks
Himani

[edsonmachado]

Hi all.

I was getting the same problem and solve by changing de .gff reference file by .fna file.

Good luck