Web Service Connection Problem

Hi,

I'm a regular user of Jalview and have used over 1.5 year and currently using anywhere installed version 2.8. I am not able to access web services and gets error message when open the program.
I use Mac OS X 10.8.3 and Win7 64bit in parallel and tried to run jalview on both the OS.
I have upgraded my java version but still does't help!
Kindly let me know how to fix this issue.

Thank you!

Error message:
"Failed to submit sequences for alignment.
Just close the window"

Java console (Mac)

Jalview Desktop 2.8
Build Date: 12 November 2012
Java version: 1.7.0_21
x86_64 Mac OS X 10.8.3
WARN - Exception when discovering One Way services:
WARN - Exception when discovering One Way services:
INFO - Not enabling Google Tracking.
INFO - Constructing news reader.
INFO - Completed construction of reader.
INFO - Saved last read date as Apr 18, 2013 1:02:08 PM
INFO - Saved last read date as Apr 18, 2013 1:02:08 PM
INFO - Saved last read date as Apr 18, 2013 1:02:08 PM

Java console windows (opens by default on startup)


Jalview Desktop 2.8
Build Date: 12 November 2012
Java version: 1.6.0_01
x86 Windows Vista 6.1
WARN - Exception when discovering One Way services:
WARN - Exception when discovering One Way services:
May 3, 2013 8:53:11 PM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!
Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service JronnWS:
Could not connect to http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl the server is down?
java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl the server is down?
at compbio.ws.client.Jws2Client.connect(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150)
at java.lang.Thread.run(Unknown Source)
Connecting to JABAWS version 2 service
Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service DisemblWS:
Could not connect to http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl the server is down?
java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl the server is down?
at compbio.ws.client.Jws2Client.connect(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150)
at java.lang.Thread.run(Unknown Source)
Connecting to JABAWS version 2 service
Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service GlobPlotWS:
Could not connect to http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl the server is down?
java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl the server is down?
at compbio.ws.client.Jws2Client.connect(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150)
at java.lang.Thread.run(Unknown Source)
Warning - overwriting a sequenceSetId for a viewport!
Building ws menu again Thread[Thread-19,5,main]
Connecting to JABAWS version 2 service
WARN - Exception when discovering Jws2 services.
Connecting to JABAWS version 2 service
Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service IUPredWS:
Could not connect to http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl the server is down?
java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl the server is down?
at compbio.ws.client.Jws2Client.connect(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150)
at java.lang.Thread.run(Unknown Source)
Connecting to JABAWS version 2 service
Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service AAConWS:
Could not connect to http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl the server is down?
java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl the server is down?
at compbio.ws.client.Jws2Client.connect(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150)
at java.lang.Thread.run(Unknown Source)
1822 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.2.4 2011-10-11 21:29
java.vendor: Sun Microsystems Inc.
java.version: 1.6.0_01
os.name: Windows Vista
memory: 22.3/33.8
processors available: 2
useCommandThread: false
May 3, 2013 8:53:13 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!

FileManager.getAtomSetCollectionFromFile(C:\\Users\\GANESH~1\\AppData\\Local\\Temp\\jalview_pdb24017.txt)
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@640f1a
FileManager opening C:\Users\GANESH~1\AppData\Local\Temp\jalview_pdb24017.txt
The Resolver thinks Pdb
java.lang.NullPointerException
at jalview.ws.jws2.Jws2Discoverer.addService(Jws2Discoverer.java:253)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:181)
at java.lang.Thread.run(Unknown Source)
Setting space group name to P 21 21 21
openFile(C:\\Users\\GANESH~1\\AppData\\Local\\Temp\\jalview_pdb24017.txt): 116 ms
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
Time to autoBond: 13 ms
ModelSet: autobonding; use autobond=false to not generate bonds automatically
Rebuild WS Menu for service change
Building ws menu again Thread[Thread-26,6,main]
ColorManager: color "roygb" range 0.0 0.0
measurement[0] = [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
History on;
Warning - overwriting a sequenceSetId for a viewport!
Building ws menu again Thread[Thread-32,5,main]
header key X-DAS-Server=[regrest/1.5]
header key Content-Type=[application/xml]
header key Date=[Fri, 03 May 2013 18:53:12 GMT]
header key Access-Control-Allow-Origin=[*]
header key X-DAS-Status=[200]
header key Transfer-Encoding=[chunked]
header key X-OSSProxy=[OSSProxy 1.3.335.337 (Build 335.337 Win32 en-us)(Apr 4 2013 16:51:42)]
header key Connection=[keep-alive]
Added another sequence DB source for Anolis_carolinensis.AnoCar2.0.reference (Anolis_carolinensis.AnoCar2.0.reference (AnoCar Contig 2.0) (DAS))
Added another sequence DB source for Anolis_carolinensis.AnoCar2.0.reference (Anolis_carolinensis.AnoCar2.0.reference (AnoCar Scaffold 2.0) (DAS))
Added another sequence DB source for Bos_taurus.UMD3.1.reference (Bos_taurus.UMD3.1.reference (UMD Scaffold 3.1) (DAS))
Added another sequence DB source for Callithrix_jacchus.C_jacchus3.2.1.reference (Callithrix_jacchus.C_jacchus3.2.1.reference (C_jacchus Chromosome 3.2.1) (DAS))
Added another sequence DB source for Choloepus_hoffmanni.choHof1.reference (Choloepus_hoffmanni.choHof1.reference (choHof Gene Scaffold 1) (DAS))
Added another sequence DB source for Danio_rerio.Zv9.reference (Danio_rerio.Zv9.reference (Zv Scaffold 9) (DAS))
Added another sequence DB source for Dasypus_novemcinctus.dasNov2.reference (Dasypus_novemcinctus.dasNov2.reference (dasNov Scaffold 2) (DAS))
Added another sequence DB source for Dipodomys_ordii.dipOrd1.reference (Dipodomys_ordii.dipOrd1.reference (dipOrd Scaffold 1) (DAS))
Building ws menu again Thread[Thread-41,5,main]
Warning - overwriting a sequenceSetId for a viewport!
Added another sequence DB source for Echinops_telfairi.TENREC.reference (Echinops_telfairi.TENREC.reference (TENREC Scaffold) (DAS))
Added another sequence DB source for Erinaceus_europaeus.HEDGEHOG.reference (Erinaceus_europaeus.HEDGEHOG.reference (HEDGEHOG Scaffold) (DAS))
Added another sequence DB source for Felis_catus.CAT.reference (Felis_catus.CAT.reference (CAT Gene Scaffold) (DAS))
Added another sequence DB source for Gadus_morhua.gadMor1.reference (Gadus_morhua.gadMor1.reference (gadMor Gene Scaffold 1) (DAS))
Added another sequence DB source for Gadus_morhua.gadMor1.reference (Gadus_morhua.gadMor1.reference (gadMor Scaffold 1) (DAS))
Added another sequence DB source for Gasterosteus_aculeatus.BROADS1.reference (Gasterosteus_aculeatus.BROADS1.reference (BROADS Scaffold 1) (DAS))
Added another sequence DB source for Homo_sapiens.GRCh37.reference (Homo_sapiens.GRCh37.reference (GRCh Chromosome 37) (DAS))
Building ws menu again Thread[Thread-52,5,main]
Warning - overwriting a sequenceSetId for a viewport!
Added another sequence DB source for Macaca_mulatta.MMUL_1.reference (Macaca_mulatta.MMUL_1.reference (MMUL Chromosome 1) (DAS))
Added another sequence DB source for Macropus_eugenii.Meug_1.0.reference (Macropus_eugenii.Meug_1.0.reference (Meug Scaffold 1.0) (DAS))
Added another sequence DB source for Meleagris_gallopavo.UMD2.reference (Meleagris_gallopavo.UMD2.reference (UMD Scaffold 2) (DAS))
Added another sequence DB source for Meleagris_gallopavo.UMD2.reference (Meleagris_gallopavo.UMD2.reference (UMD Contig 2) (DAS))
Added another sequence DB source for Microcebus_murinus.micMur1.reference (Microcebus_murinus.micMur1.reference (micMur Scaffold 1) (DAS))
Added another sequence DB source for Mus_musculus.NCBIM37.reference (Mus_musculus.NCBIM37.reference (NCBIM Supercontig 37) (DAS))
Added anotheINFO - Not enabling Google Tracking.
r sequence DB source for Nomascus_leucogenys.Nleu1.0.reference (Nomascus_leucogenys.Nleu1.0.reference (Nleu Contig 1.0) (DAS))
Added another sequence DB source for Ochotona_princeps.pika.reference (Ochotona_princeps.pika.reference (pika Gene Scaffold) (DAS))
Building ws menu again Thread[Thread-66,5,main]
Warning - overwriting a sequenceSetId for a viewport!
Added another sequence DB source for Ornithorhynchus_anatinus.OANA5.reference (Ornithorhynchus_anatinus.OANA5.reference (OANA Ultracontig 5) (DAS))
Added another sequence DB source for Ornithorhynchus_anatinus.OANA5.reference (Ornithorhynchus_anatinus.OANA5.reference (OANA Supercontig 5) (DAS))
Added another sequence DB source for Oryctolagus_cuniculus.oryCun2.reference (Oryctolagus_cuniculus.oryCun2.reference (oryCun Chromosome 2) (DAS))
Added another sequence DB source for Oryzias_latipes.MEDAKA1.reference (Oryzias_latipes.MEDAKA1.reference (MEDAKA Scaffold 1) (DAS))
Added another sequence DB source for Oryzias_latipes.MEDAKA1.reference (OryziasINFO - Constructing news reader.
INFO - Completed construction of reader.
deregistering discoverer listener
deregistering discoverer listener
deregistering discoverer listener
deregistering discoverer listener
_latipes.MEDAKA1.reference (MEDAKA Chromosome 1) (DAS))
Exception occurred during event dispatching:
java.lang.ArrayIndexOutOfBoundsException: No such child: 4
at java.awt.Container.getComponent(Unknown Source)
at javax.swing.JComponent.rectangleIsObscured(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JLayeredPane.paint(Unknown Source)
at javax.swing.JComponent.paintToOffscreen(Unknown Source)
at javax.swing.BufferStrategyPaintManager.paint(Unknown Source)
at javax.swing.RepaintManager.paint(Unknown Source)
at javax.swing.JComponent._paintImmediately(Unknown Source)
at javax.swing.JComponent.paintImmediately(Unknown Source)
at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
at javax.swing.RepaintManager.seqPaintDirtyRegions(Unknown Source)
at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.Dialog$1.run(Unknown Source)
at java.awt.Dialog$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Dialog.show(Unknown Source)
at javax.swing.JOptionPane.showOptionDialog(Unknown Source)
at javax.swing.JOptionPane.showConfirmDialog(Unknown Source)
at javax.swing.JOptionPane.showConfirmDialog(Unknown Source)
at jalview.gui.Desktop$20.run(Desktop.java:2550)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Added another sequence DB source for Pan_troglodytes.CHIMP2.1.4.reference (Pan_troglodytes.CHIMP2.1.4.reference (CHIMP Chromosome 2.1.4) (DAS))
Added another sequence DB source for Procavia_capensis.proCap1.reference (Procavia_capensis.proCap1.reference (proCap Gene Scaffold 1) (DAS))
Added another sequence DB source for Pteropus_vampyrus.pteVam1.reference (Pteropus_vampyrus.pteVam1.reference (pteVam Gene Scaffold 1) (DAS))
Added another sequence DB source for Sorex_araneus.COMMON_SHREW1.reference (Sorex_araneus.COMMON_SHREW1.reference (COMMON_SHREW Gene Scaffold 1) (DAS))
Added another sequence DB source for Spermophilus_tridecemlineatus.SQUIRREL.reference (Spermophilus_tridecemlineatus.SQUIRREL.reference (SQUIRREL Gene Scaffold) (DAS))
Added another sequence DB source for Tarsius_syrichta.tarSyr1.reference (Tarsius_syrichta.tarSyr1.reference (tarSyr Scaffold 1) (DAS))
Added another sequence DB source for Tupaia_belangeri.TREESHREW.reference (Tupaia_belangeri.TREESHREW.reference (TREESHREW Scaffold) (DAS))
Added another sequence DB source for Tursiops_truncatus.turTru1.reference (Tursiops_truncatus.turTru1.reference (turTru Gene Scaffold 1) (DAS))
Added another sequence DB source for Vicugna_pacos.vicPac1.reference (Vicugna_pacos.vicPac1.reference (vicPac Gene Scaffold 1) (DAS))
Added another sequence DB source for Ciona_intestinalis.JGI2.reference (Ciona_intestinalis.JGI2.reference (JGI Chromosome 2) (DAS))
Added another sequence DB source for Bos_taurus.Btau_4.0.reference (Bos_taurus.Btau_4.0.reference (Btau Contig 4.0) (DAS))
Added another sequence DB source for Otolemur_garnettii.BUSHBABY1.reference (Otolemur_garnettii.BUSHBABY1.reference (BUSHBABY Scaffold 1) (DAS))
Added another sequence DB source for Myotis_lucifugus.MICROBAT1.reference (Myotis_lucifugus.MICROBAT1.reference (MICROBAT Scaffold 1) (DAS))
Added another sequence DB source for Danio_rerio.Zv8.reference (Danio_rerio.Zv8.reference (Zv Scaffold 8) (DAS))
Added another sequence DB source for Gorilla_gorilla.gorGor1.reference (Gorilla_gorilla.gorGor1.reference (gorGor Gene Scaffold 1) (DAS))
Added another sequence DB source for Loxodonta_africana.loxAfr2.reference (Loxodonta_africana.loxAfr2.reference (loxAfr Scaffold 2) (DAS))
Added another sequence DB source for Oryctolagus_cuniculus.RABBIT.reference (Oryctolagus_cuniculus.RABBIT.reference (RABBIT Scaffold) (DAS))
Added another sequence DB source for Homo_sapiens.NCBI36.reference (Homo_sapiens.NCBI36.reference (NCBI Supercontig 36) (DAS))
Added another sequence DB source for Danio_rerio.ZFISH7.reference (Danio_rerio.ZFISH7.reference (ZFISH Scaffold 7) (DAS))
INFO - Saved last read date as Apr 18, 2013 1:02:08 PM
INFO - Saved last read date as Apr 18, 2013 1:02:08 PM
INFO - Saved last read date as Apr 18, 2013 1:02:08 PM

Best,
Ganesh
Karolinska institutet, Stockholm