2019/10/02 11:32:26:166 INFO Using appdir from command line: .
2019/10/02 11:32:26:168 INFO Using appid from command line: jalview
2019/10/02 11:32:26:168 INFO Starting ...
2019/10/02 11:32:26:171 INFO ------------------ VM Info ------------------
2019/10/02 11:32:26:171 INFO -- OS Name: Windows 10
2019/10/02 11:32:26:171 INFO -- OS Arch: amd64
2019/10/02 11:32:26:171 INFO -- OS Vers: 10.0
2019/10/02 11:32:26:171 INFO -- Java Vers: 1.8.0_202
2019/10/02 11:32:26:172 INFO -- Java Home: c:\temp\jalview11b\jre
2019/10/02 11:32:26:172 INFO -- User Name: hansonr
2019/10/02 11:32:26:172 INFO -- User Home: C:\Users\hansonr
2019/10/02 11:32:26:172 INFO -- Cur dir: C:\temp\Jalview11b
2019/10/02 11:32:26:172 INFO -- launcher version: 1.8.3-1.1.8_JVL
2019/10/02 11:32:26:172 INFO -- startupFilesParameterString: 
2019/10/02 11:32:26:172 INFO ---------------------------------------------
2019/10/02 11:32:26:264 INFO Getdown starting [version=1.8.3-1.1.8_JVL, built=2019-07-04 12:49]
2019/10/02 11:32:26:268 INFO Failed to find proxy settings in Windows registry [error=java.lang.UnsatisfiedLinkError: no jRegistryKey in java.library.path]
2019/10/02 11:32:26:272 INFO Checking whether we need to use a proxy...
2019/10/02 11:32:26:292 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:300 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:383 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:384 INFO Keep on top set to  [keep_on_top=true]
2019/10/02 11:32:26:425 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:450 INFO Displaying instant background image
2019/10/02 11:32:26:464 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:465 WARNING Tried to invokeAndWait but couldn't. Going to invokeLater instead [Exception=null]
2019/10/02 11:32:26:470 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:593 INFO Downloading 0 resources [totalBytes=0, maxConcurrent=10]
2019/10/02 11:32:26:599 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:608 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:609 INFO Testing whether proxy is needed, via: http://www.jalview.org/getdown/release/1.8/getdown.txt
2019/10/02 11:32:26:736 INFO No proxy appears to be needed.
2019/10/02 11:32:26:740 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:744 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:745 INFO Downloading 0 resources [totalBytes=0, maxConcurrent=10]
2019/10/02 11:32:26:748 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:761 INFO Able to lock for updates: true
2019/10/02 11:32:26:765 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:766 INFO Verifying application: http://www.jalview.org/getdown/release/1.8/
2019/10/02 11:32:26:767 INFO Version: -1
2019/10/02 11:32:26:767 INFO Class: jalview.bin.Jalview
2019/10/02 11:32:26:783 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:783 INFO Attempting to refetch 'digest.txt' from 'http://www.jalview.org/getdown/release/1.8/digest.txt'.
2019/10/02 11:32:26:830 INFO No signing certs, not verifying digest.txt [path=digest.txt]
2019/10/02 11:32:26:832 INFO Attempting to refetch 'digest2.txt' from 'http://www.jalview.org/getdown/release/1.8/digest2.txt'.
2019/10/02 11:32:26:876 INFO No signing certs, not verifying digest.txt [path=digest2.txt]
2019/10/02 11:32:26:883 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:900 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:903 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:905 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:908 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:923 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:927 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:929 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:931 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:933 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:935 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:937 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:939 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:943 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:946 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:948 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:950 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:952 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:955 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:957 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:959 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:962 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:970 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:972 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:974 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:977 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:979 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:981 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:983 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:985 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:987 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:989 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:992 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:996 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:26:999 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:003 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:005 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:008 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:013 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:017 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:019 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:021 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:023 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:027 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:029 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:034 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:036 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:038 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:039 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:042 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:044 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:046 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:047 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:049 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:050 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:052 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:054 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:055 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:057 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:059 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:061 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:062 INFO Verified resources [count=60, size=36550k, duration=177ms]
2019/10/02 11:32:27:063 INFO Checking Java version [current=1080202, wantMin=1080000, wantMax=1089999]
2019/10/02 11:32:27:063 INFO vmfile is 'jre.tgz'
vmfile is 'jre.tgz'
2019/10/02 11:32:27:064 INFO Attempting to fetch jvm at http://www.jalview.org/getdown/jre/windows-jre1.8.tgz
Attempting to fetch jvm at http://www.jalview.org/getdown/jre/windows-jre1.8.tgz
2019/10/02 11:32:27:064 INFO Installing 0 downloaded resources:
2019/10/02 11:32:27:064 INFO Install completed.
2019/10/02 11:32:27:065 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
2019/10/02 11:32:27:068 INFO Didn't find any custom environment variables, not setting any.
2019/10/02 11:32:27:068 INFO Running C:\temp\Jalview11b\.\jre\bin\java.exe
  -classpath
  C:\temp\Jalview11b\.\release\JGoogleAnalytics_0.3.jar;C:\temp\Jalview11b\.\release\Jmol-14.6.4_2016.10.26.jar;C:\temp\Jalview11b\.\release\VARNAv3-93.jar;C:\temp\Jalview11b\.\release\VAqua5-patch.jar;C:\temp\Jalview11b\.\release\activation.jar;C:\temp\Jalview11b\.\release\apache-mime4j-0.6.jar;C:\temp\Jalview11b\.\release\axis.jar;C:\temp\Jalview11b\.\release\biojava-core-4.1.0.jar;C:\temp\Jalview11b\.\release\biojava-ontology-4.1.0.jar;C:\temp\Jalview11b\.\release\commons-codec-1.3.jar;C:\temp\Jalview11b\.\release\commons-compress-1.18.jar;C:\temp\Jalview11b\.\release\commons-discovery.jar;C:\temp\Jalview11b\.\release\commons-logging-1.1.1.jar;C:\temp\Jalview11b\.\release\getdown-core.jar;C:\temp\Jalview11b\.\release\groovy-all-2.4.12-indy.jar;C:\temp\Jalview11b\.\release\htsjdk-2.12.0.jar;C:\temp\Jalview11b\.\release\httpclient-4.0.3.jar;C:\temp\Jalview11b\.\release\httpcore-4.0.1.jar;C:\temp\Jalview11b\.\release\httpmime-4.0.3.jar;C:\temp\Jalview11b\.\release\intervalstore-v1.0.jar;C:\temp\Jalview11b\.\release\jabaws-min-client-2.2.0.jar;C:\temp\Jalview11b\.\release\jalview.jar;C:\temp\Jalview11b\.\release\java-json.jar;C:\temp\Jalview11b\.\release\jaxrpc.jar;C:\temp\Jalview11b\.\release\jersey-client-1.19.4.jar;C:\temp\Jalview11b\.\release\jersey-core-1.19.4.jar;C:\temp\Jalview11b\.\release\jersey-json-1.19.4.jar;C:\temp\Jalview11b\.\release\jetty-http-9.2.10.v20150310.jar;C:\temp\Jalview11b\.\release\jetty-io-9.2.10.v20150310.jar;C:\temp\Jalview11b\.\release\jetty-server-9.2.10.v20150310.jar;C:\temp\Jalview11b\.\release\jetty-util-9.2.10.v20150310.jar;C:\temp\Jalview11b\.\release\jfreesvg-2.1.jar;C:\temp\Jalview11b\.\release\jhall.jar;C:\temp\Jalview11b\.\release\json_simple-1.1.jar;C:\temp\Jalview11b\.\release\jsoup-1.8.1.jar;C:\temp\Jalview11b\.\release\jsr311-api-1.1.1.jar;C:\temp\Jalview11b\.\release\jswingreader-0.3.jar;C:\temp\Jalview11b\.\release\libquaqua-8.0.jnilib.jar;C:\temp\Jalview11b\.\release\libquaqua64-8.0.jnilib.jar;C:\temp\Jalview11b\.\release\log4j-to-slf4j-2.0-rc2.jar;C:\temp\Jalview11b\.\release\mail.jar;C:\temp\Jalview11b\.\release\miglayout-4.0-swing.jar;C:\temp\Jalview11b\.\release\quaqua-filechooser-only-8.0.jar;C:\temp\Jalview11b\.\release\regex.jar;C:\temp\Jalview11b\.\release\saaj.jar;C:\temp\Jalview11b\.\release\servlet-api-3.1.jar;C:\temp\Jalview11b\.\release\slf4j-api-1.7.7.jar;C:\temp\Jalview11b\.\release\slf4j-log4j12-1.7.7.jar;C:\temp\Jalview11b\.\release\vamsas-client.jar;C:\temp\Jalview11b\.\release\wsdl4j.jar;C:\temp\Jalview11b\.\release\xercesImpl.jar;C:\temp\Jalview11b\.\release\xml-apis.jar
  -Dcom.threerings.getdown=true
  -Dgetdownappdir=C:\temp\Jalview11b\.
  -Xmx7175356416
  jalview.bin.Jalview
Ignoring SO:0001957 as obsolete and duplicated by SO:0001979Ignoring SO:0000437 as obsolete and duplicated by SO:0000800Ignoring SO:0000554 as obsolete and duplicated by SO:0000801Ignoring SO:0000767 as obsolete and duplicated by SO:0000179Ignoring SO:0000058 as obsolete and duplicated by SO:0000803Ignoring SO:0001052 as obsolete and duplicated by SO:0001649Ignoring SO:0000052 as obsolete and duplicated by SO:0000802Ignoring SO:0001053 as obsolete and duplicated by SO:0001648Oct 02, 2019 11:32:27 AM jalview.util.MessageManager <clinit>INFO: Getting messages for lang: en_USOct 02, 2019 11:32:29 AM compbio.ws.client.Jws2Client connectToRegistryINFO: Connected to RegistryWS successfully!Oct 02, 2019 11:32:29 AM compbio.ws.client.Jws2Client connectINFO: Connected successfully!Oct 02, 2019 11:32:29 AM compbio.ws.client.Jws2Client connectINFO: Connected successfully!Oct 02, 2019 11:32:30 AM compbio.ws.client.Jws2Client connectINFO: Connected successfully!Oct 02, 2019 11:32:30 AM compbio.ws.client.Jws2Client connectINFO: Connected successfully!Warning - overwriting a sequenceSetId for a viewport!Oct 02, 2019 11:32:30 AM compbio.ws.client.Jws2Client connectINFO: Connected successfully!Oct 02, 2019 11:32:31 AM compbio.ws.client.Jws2Client connectINFO: Connected successfully!2019/10/02 11:32:32:266 INFO Max memory set [maxMemHeapArg=-Xmx7175356416]
Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665]Oct 02, 2019 11:32:32 AM compbio.ws.client.Jws2Client connectINFO: Connected successfully!