2014-02-23T17:05:14 1393193114353 0 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Java version: 1.7.0_51 2014-02-23T17:05:14 1393193114361 1 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 amd64 Windows 7 6.1 2014-02-23T17:05:14 1393193114462 2 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Jalview Version: 2.8.0b1 2014-02-23T17:05:14 1393193114482 3 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 # INFO: Setting default net timeout to 30 seconds. 2014-02-23T17:05:15 1393193115697 4 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 WARN : jalview.bin.Jalview - Exception when discovering One Way services: java.io.IOException: Server returned HTTP response code: 500 for URL: http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at java.net.URL.openStream(Unknown Source) at jalview.ws.EnfinEnvision2OneWay.run(EnfinEnvision2OneWay.java:244) at java.lang.Thread.run(Unknown Source) 2014-02-23T17:05:15 1393193115719 5 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 WARN - Exception when discovering One Way services: java.io.IOException: Server returned HTTP response code: 500 for URL: http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at java.net.URL.openStream(Unknown Source) at jalview.ws.EnfinEnvision2OneWay.run(EnfinEnvision2OneWay.java:244) at java.lang.Thread.run(Unknown Source) 2014-02-23T17:05:15 1393193115885 6 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 WARN : jalview.bin.Jalview - Exception when discovering One Way services: java.io.IOException: Server returned HTTP response code: 500 for URL: http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at java.net.URL.openStream(Unknown Source) at jalview.ws.EnfinEnvision2OneWay.run(EnfinEnvision2OneWay.java:244) at java.lang.Thread.run(Unknown Source) 2014-02-23T17:05:16 1393193116009 7 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 WARN - Exception when discovering One Way services: java.io.IOException: Server returned HTTP response code: 500 for URL: http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at java.net.URL.openStream(Unknown Source) at jalview.ws.EnfinEnvision2OneWay.run(EnfinEnvision2OneWay.java:244) at java.lang.Thread.run(Unknown Source) 2014-02-23T17:05:16 1393193116150 9 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Feb 23, 2014 5:05:16 PM compbio.ws.client.Jws2Client connectToRegistry INFO: Connected to RegistryWS successfully! 2014-02-23T17:05:17 1393193117095 10 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Connecting to JABAWS version 2 service 2014-02-23T17:05:17 1393193117623 12 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Feb 23, 2014 5:05:17 PM compbio.ws.client.Jws2Client connect INFO: Connected successfully! 2014-02-23T17:05:17 1393193117883 13 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@5dbd5a2c 2014-02-23T17:05:19 1393193119013 14 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Connecting to JABAWS version 2 service 2014-02-23T17:05:19 1393193119404 16 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Feb 23, 2014 5:05:19 PM compbio.ws.client.Jws2Client connect INFO: Connected successfully! 2014-02-23T17:05:21 1393193121130 17 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO : jalview.bin.Jalview - Not enabling Google Tracking. 2014-02-23T17:05:21 1393193121131 18 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO - Not enabling Google Tracking. 2014-02-23T17:05:21 1393193121195 19 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO : jalview.bin.Jalview - Constructing news reader. 2014-02-23T17:05:21 1393193121198 20 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO - Constructing news reader. 2014-02-23T17:05:21 1393193121505 21 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 CacheEntry[http://www.jalview.org/feeds/desktop/rss]: updateAvailable=true,lastModified=Sun Feb 23 16:29:41 EST 2014,length=12728 2014-02-23T17:05:21 1393193121921 22 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO : jalview.bin.Jalview - Completed construction of reader. 2014-02-23T17:05:21 1393193121934 23 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO - Completed construction of reader. 2014-02-23T17:05:26 1393193126242 24 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO : jalview.bin.Jalview - Saved last read date as Jan 31, 2014 7:45:46 AM 2014-02-23T17:05:26 1393193126248 25 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO - Saved last read date as Jan 31, 2014 7:45:46 AM 2014-02-23T17:05:26 1393193126258 26 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO : jalview.bin.Jalview - Saved last read date as Jan 31, 2014 7:45:46 AM 2014-02-23T17:05:26 1393193126261 27 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO - Saved last read date as Jan 31, 2014 7:45:46 AM 2014-02-23T17:05:26 1393193126265 28 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO : jalview.bin.Jalview - Saved last read date as Jan 31, 2014 7:45:46 AM 2014-02-23T17:05:26 1393193126269 29 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 INFO - Saved last read date as Jan 31, 2014 7:45:46 AM 2014-02-23T17:05:27 1393193127774 30 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Building ws menu again Thread[Thread-37,6,javawsApplicationThreadGroup] 2014-02-23T17:05:29 1393193129777 31 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 header key X-DAS-Server=[regrest/1.5] 2014-02-23T17:05:29 1393193129777 32 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 header key Content-Type=[application/xml] 2014-02-23T17:05:29 1393193129897 33 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 header key Date=[Sun, 23 Feb 2014 22:05:28 GMT] 2014-02-23T17:05:29 1393193129930 34 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 header key Transfer-Encoding=[chunked] 2014-02-23T17:05:29 1393193129932 35 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 header key Access-Control-Allow-Origin=[*] 2014-02-23T17:05:29 1393193129935 36 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 header key X-DAS-Status=[200] 2014-02-23T17:05:29 1393193129938 37 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Anolis_carolinensis.AnoCar2.0.reference (Anolis_carolinensis.AnoCar2.0.reference (AnoCar Contig 2.0) (DAS)) 2014-02-23T17:05:29 1393193129941 38 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Anolis_carolinensis.AnoCar2.0.reference (Anolis_carolinensis.AnoCar2.0.reference (AnoCar Scaffold 2.0) (DAS)) 2014-02-23T17:05:29 1393193129944 39 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Bos_taurus.UMD3.1.reference (Bos_taurus.UMD3.1.reference (UMD Scaffold 3.1) (DAS)) 2014-02-23T17:05:29 1393193129947 40 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 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)) 2014-02-23T17:05:29 1393193129975 41 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Choloepus_hoffmanni.choHof1.reference (Choloepus_hoffmanni.choHof1.reference (choHof Gene Scaffold 1) (DAS)) 2014-02-23T17:05:29 1393193129978 42 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Danio_rerio.Zv9.reference (Danio_rerio.Zv9.reference (Zv Scaffold 9) (DAS)) 2014-02-23T17:05:29 1393193129980 43 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Dasypus_novemcinctus.dasNov2.reference (Dasypus_novemcinctus.dasNov2.reference (dasNov Scaffold 2) (DAS)) 2014-02-23T17:05:29 1393193129984 44 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Dipodomys_ordii.dipOrd1.reference (Dipodomys_ordii.dipOrd1.reference (dipOrd Scaffold 1) (DAS)) 2014-02-23T17:05:29 1393193129987 45 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Echinops_telfairi.TENREC.reference (Echinops_telfairi.TENREC.reference (TENREC Scaffold) (DAS)) 2014-02-23T17:05:29 1393193129990 46 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Erinaceus_europaeus.HEDGEHOG.reference (Erinaceus_europaeus.HEDGEHOG.reference (HEDGEHOG Scaffold) (DAS)) 2014-02-23T17:05:29 1393193129993 47 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Felis_catus.CAT.reference (Felis_catus.CAT.reference (CAT Gene Scaffold) (DAS)) 2014-02-23T17:05:29 1393193129996 48 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Gadus_morhua.gadMor1.reference (Gadus_morhua.gadMor1.reference (gadMor Gene Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130003 49 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Gadus_morhua.gadMor1.reference (Gadus_morhua.gadMor1.reference (gadMor Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130031 50 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Gasterosteus_aculeatus.BROADS1.reference (Gasterosteus_aculeatus.BROADS1.reference (BROADS Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130041 51 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Homo_sapiens.GRCh37.reference (Homo_sapiens.GRCh37.reference (GRCh Chromosome 37) (DAS)) 2014-02-23T17:05:30 1393193130043 52 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Macaca_mulatta.MMUL_1.reference (Macaca_mulatta.MMUL_1.reference (MMUL Chromosome 1) (DAS)) 2014-02-23T17:05:30 1393193130056 53 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Macropus_eugenii.Meug_1.0.reference (Macropus_eugenii.Meug_1.0.reference (Meug Scaffold 1.0) (DAS)) 2014-02-23T17:05:30 1393193130058 54 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Meleagris_gallopavo.UMD2.reference (Meleagris_gallopavo.UMD2.reference (UMD Scaffold 2) (DAS)) 2014-02-23T17:05:30 1393193130065 55 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Meleagris_gallopavo.UMD2.reference (Meleagris_gallopavo.UMD2.reference (UMD Contig 2) (DAS)) 2014-02-23T17:05:30 1393193130068 56 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Microcebus_murinus.micMur1.reference (Microcebus_murinus.micMur1.reference (micMur Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130075 57 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Mus_musculus.NCBIM37.reference (Mus_musculus.NCBIM37.reference (NCBIM Supercontig 37) (DAS)) 2014-02-23T17:05:30 1393193130078 58 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Nomascus_leucogenys.Nleu1.0.reference (Nomascus_leucogenys.Nleu1.0.reference (Nleu Contig 1.0) (DAS)) 2014-02-23T17:05:30 1393193130090 59 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Ochotona_princeps.pika.reference (Ochotona_princeps.pika.reference (pika Gene Scaffold) (DAS)) 2014-02-23T17:05:30 1393193130092 60 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Ornithorhynchus_anatinus.OANA5.reference (Ornithorhynchus_anatinus.OANA5.reference (OANA Ultracontig 5) (DAS)) 2014-02-23T17:05:30 1393193130095 61 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Ornithorhynchus_anatinus.OANA5.reference (Ornithorhynchus_anatinus.OANA5.reference (OANA Supercontig 5) (DAS)) 2014-02-23T17:05:30 1393193130097 62 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Oryctolagus_cuniculus.oryCun2.reference (Oryctolagus_cuniculus.oryCun2.reference (oryCun Chromosome 2) (DAS)) 2014-02-23T17:05:30 1393193130101 63 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Oryzias_latipes.MEDAKA1.reference (Oryzias_latipes.MEDAKA1.reference (MEDAKA Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130104 64 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Oryzias_latipes.MEDAKA1.reference (Oryzias_latipes.MEDAKA1.reference (MEDAKA Chromosome 1) (DAS)) 2014-02-23T17:05:30 1393193130107 65 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Pan_troglodytes.CHIMP2.1.4.reference (Pan_troglodytes.CHIMP2.1.4.reference (CHIMP Chromosome 2.1.4) (DAS)) 2014-02-23T17:05:30 1393193130111 66 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Procavia_capensis.proCap1.reference (Procavia_capensis.proCap1.reference (proCap Gene Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130114 67 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Pteropus_vampyrus.pteVam1.reference (Pteropus_vampyrus.pteVam1.reference (pteVam Gene Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130120 68 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Sorex_araneus.COMMON_SHREW1.reference (Sorex_araneus.COMMON_SHREW1.reference (COMMON_SHREW Gene Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130126 69 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Spermophilus_tridecemlineatus.SQUIRREL.reference (Spermophilus_tridecemlineatus.SQUIRREL.reference (SQUIRREL Gene Scaffold) (DAS)) 2014-02-23T17:05:30 1393193130129 70 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Tarsius_syrichta.tarSyr1.reference (Tarsius_syrichta.tarSyr1.reference (tarSyr Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130131 71 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Tupaia_belangeri.TREESHREW.reference (Tupaia_belangeri.TREESHREW.reference (TREESHREW Scaffold) (DAS)) 2014-02-23T17:05:30 1393193130134 72 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Tursiops_truncatus.turTru1.reference (Tursiops_truncatus.turTru1.reference (turTru Gene Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130136 73 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Vicugna_pacos.vicPac1.reference (Vicugna_pacos.vicPac1.reference (vicPac Gene Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130138 74 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Ciona_intestinalis.JGI2.reference (Ciona_intestinalis.JGI2.reference (JGI Chromosome 2) (DAS)) 2014-02-23T17:05:30 1393193130140 75 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Bos_taurus.Btau_4.0.reference (Bos_taurus.Btau_4.0.reference (Btau Contig 4.0) (DAS)) 2014-02-23T17:05:30 1393193130143 76 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Otolemur_garnettii.BUSHBABY1.reference (Otolemur_garnettii.BUSHBABY1.reference (BUSHBABY Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130145 77 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Myotis_lucifugus.MICROBAT1.reference (Myotis_lucifugus.MICROBAT1.reference (MICROBAT Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130147 78 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Danio_rerio.Zv8.reference (Danio_rerio.Zv8.reference (Zv Scaffold 8) (DAS)) 2014-02-23T17:05:30 1393193130150 79 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Gorilla_gorilla.gorGor1.reference (Gorilla_gorilla.gorGor1.reference (gorGor Gene Scaffold 1) (DAS)) 2014-02-23T17:05:30 1393193130152 80 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Loxodonta_africana.loxAfr2.reference (Loxodonta_africana.loxAfr2.reference (loxAfr Scaffold 2) (DAS)) 2014-02-23T17:05:30 1393193130154 81 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Oryctolagus_cuniculus.RABBIT.reference (Oryctolagus_cuniculus.RABBIT.reference (RABBIT Scaffold) (DAS)) 2014-02-23T17:05:30 1393193130156 82 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Homo_sapiens.NCBI36.reference (Homo_sapiens.NCBI36.reference (NCBI Supercontig 36) (DAS)) 2014-02-23T17:05:30 1393193130159 83 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Added another sequence DB source for Danio_rerio.ZFISH7.reference (Danio_rerio.ZFISH7.reference (ZFISH Scaffold 7) (DAS)) 2014-02-23T17:05:41 1393193141150 84 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 javax.xml.ws.WebServiceException: java.net.SocketTimeoutException: Read timed out 2014-02-23T17:05:41 1393193141200 85 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.transport.http.client.HttpClientTransport.readResponseCodeAndMessage(Unknown Source) 2014-02-23T17:05:41 1393193141203 86 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.createResponsePacket(Unknown Source) 2014-02-23T17:05:41 1393193141207 87 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.process(Unknown Source) 2014-02-23T17:05:41 1393193141211 88 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.processRequest(Unknown Source) 2014-02-23T17:05:41 1393193141214 89 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.transport.DeferredTransportPipe.processRequest(Unknown Source) 2014-02-23T17:05:41 1393193141217 90 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.api.pipe.Fiber.__doRun(Unknown Source) 2014-02-23T17:05:41 1393193141220 91 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.api.pipe.Fiber._doRun(Unknown Source) 2014-02-23T17:05:41 1393193141223 92 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.api.pipe.Fiber.doRun(Unknown Source) 2014-02-23T17:05:41 1393193141227 93 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.api.pipe.Fiber.runSync(Unknown Source) 2014-02-23T17:05:41 1393193141230 94 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.client.Stub.process(Unknown Source) 2014-02-23T17:05:41 1393193141233 95 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.client.sei.SEIStub.doProcess(Unknown Source) 2014-02-23T17:05:41 1393193141236 96 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source) 2014-02-23T17:05:41 1393193141239 97 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source) 2014-02-23T17:05:41 1393193141243 98 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(Unknown Source) 2014-02-23T17:05:41 1393193141246 99 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at com.sun.proxy.$Proxy19.getServiceDescription(Unknown Source) 2014-02-23T17:05:41 1393193141248 100 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:172) 2014-02-23T17:05:41 1393193141298 101 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at java.lang.Thread.run(Unknown Source) 2014-02-23T17:05:41 1393193141301 102 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Caused by: java.net.SocketTimeoutException: Read timed out 2014-02-23T17:05:41 1393193141306 103 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at java.net.SocketInputStream.socketRead0(Native Method) 2014-02-23T17:05:41 1393193141309 104 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at java.net.SocketInputStream.read(Unknown Source) 2014-02-23T17:05:41 1393193141314 105 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at java.net.SocketInputStream.read(Unknown Source) 2014-02-23T17:05:41 1393193141319 106 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at java.io.BufferedInputStream.fill(Unknown Source) 2014-02-23T17:05:41 1393193141326 107 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at java.io.BufferedInputStream.read1(Unknown Source) 2014-02-23T17:05:41 1393193141334 108 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at java.io.BufferedInputStream.read(Unknown Source) 2014-02-23T17:05:41 1393193141336 109 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at sun.net.www.http.HttpClient.parseHTTPHeader(Unknown Source) 2014-02-23T17:05:41 1393193141340 110 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at sun.net.www.http.HttpClient.parseHTTP(Unknown Source) 2014-02-23T17:05:41 1393193141373 111 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) 2014-02-23T17:05:41 1393193141378 112 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 at java.net.HttpURLConnection.getResponseCode(Unknown Source) 2014-02-23T17:05:41 1393193141382 113 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 ... 17 more 2014-02-23T17:05:41 1393193141385 114 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 WARN : jalview.bin.Jalview - Exception when discovering Jws2 services. javax.xml.ws.WebServiceException: java.net.SocketTimeoutException: Read timed out at com.sun.xml.internal.ws.transport.http.client.HttpClientTransport.readResponseCodeAndMessage(Unknown Source) at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.createResponsePacket(Unknown Source) at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.process(Unknown Source) at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.processRequest(Unknown Source) at com.sun.xml.internal.ws.transport.DeferredTransportPipe.processRequest(Unknown Source) at com.sun.xml.internal.ws.api.pipe.Fiber.__doRun(Unknown Source) at com.sun.xml.internal.ws.api.pipe.Fiber._doRun(Unknown Source) at com.sun.xml.internal.ws.api.pipe.Fiber.doRun(Unknown Source) at com.sun.xml.internal.ws.api.pipe.Fiber.runSync(Unknown Source) at com.sun.xml.internal.ws.client.Stub.process(Unknown Source) at com.sun.xml.internal.ws.client.sei.SEIStub.doProcess(Unknown Source) at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source) at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source) at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(Unknown Source) at com.sun.proxy.$Proxy19.getServiceDescription(Unknown Source) at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:172) at java.lang.Thread.run(Unknown Source) Caused by: java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.io.BufferedInputStream.fill(Unknown Source) at java.io.BufferedInputStream.read1(Unknown Source) at java.io.BufferedInputStream.read(Unknown Source) at sun.net.www.http.HttpClient.parseHTTPHeader(Unknown Source) at sun.net.www.http.HttpClient.parseHTTP(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at java.net.HttpURLConnection.getResponseCode(Unknown Source) ... 17 more 2014-02-23T17:05:41 1393193141404 115 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 WARN - Exception when discovering Jws2 services. javax.xml.ws.WebServiceException: java.net.SocketTimeoutException: Read timed out at com.sun.xml.internal.ws.transport.http.client.HttpClientTransport.readResponseCodeAndMessage(Unknown Source) at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.createResponsePacket(Unknown Source) at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.process(Unknown Source) at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.processRequest(Unknown Source) at com.sun.xml.internal.ws.transport.DeferredTransportPipe.processRequest(Unknown Source) at com.sun.xml.internal.ws.api.pipe.Fiber.__doRun(Unknown Source) at com.sun.xml.internal.ws.api.pipe.Fiber._doRun(Unknown Source) at com.sun.xml.internal.ws.api.pipe.Fiber.doRun(Unknown Source) at com.sun.xml.internal.ws.api.pipe.Fiber.runSync(Unknown Source) at com.sun.xml.internal.ws.client.Stub.process(Unknown Source) at com.sun.xml.internal.ws.client.sei.SEIStub.doProcess(Unknown Source) at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source) at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(Unknown Source) at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(Unknown Source) at com.sun.proxy.$Proxy19.getServiceDescription(Unknown Source) at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:172) at java.lang.Thread.run(Unknown Source) Caused by: java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.io.BufferedInputStream.fill(Unknown Source) at java.io.BufferedInputStream.read1(Unknown Source) at java.io.BufferedInputStream.read(Unknown Source) at sun.net.www.http.HttpClient.parseHTTPHeader(Unknown Source) at sun.net.www.http.HttpClient.parseHTTP(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at java.net.HttpURLConnection.getResponseCode(Unknown Source) ... 17 more 2014-02-23T17:05:41 1393193141409 116 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Rebuild WS Menu for service change 2014-02-23T17:05:41 1393193141414 117 com.sun.deploy FINE com.sun.deploy.trace.LoggerTraceListener print 9 Building ws menu again Thread[Thread-40,6,javawsApplicationThreadGroup]