2019/08/16 11:35:41:211 INFO Using appdir from command line: .
2019/08/16 11:35:41:212 INFO Using appid from command line: jalview
2019/08/16 11:35:41:212 INFO Starting ...
2019/08/16 11:35:41:540 INFO ------------------ VM Info ------------------
2019/08/16 11:35:41:540 INFO -- OS Name: Mac OS X
2019/08/16 11:35:41:540 INFO -- OS Arch: x86_64
2019/08/16 11:35:41:540 INFO -- OS Vers: 10.13.6
2019/08/16 11:35:41:540 INFO -- Java Vers: 1.8.0_202
2019/08/16 11:35:41:540 INFO -- Java Home: /Applications/Jalview_real.app/Contents/Resources/app/jre/Contents/Home
2019/08/16 11:35:41:540 INFO -- User Name: jprocter
2019/08/16 11:35:41:540 INFO -- User Home: /Users/jprocter
2019/08/16 11:35:41:540 INFO -- Cur dir: /Applications/Jalview_real.app/Contents/Resources/app
2019/08/16 11:35:41:541 INFO -- launcher version: 1.8.3-1.1.8_JVL
2019/08/16 11:35:41:541 INFO -- startupFilesParameterString: 
2019/08/16 11:35:41:541 INFO ---------------------------------------------
2019/08/16 11:35:41:569 INFO Getdown starting [version=1.8.3-1.1.8_JVL, built=2019-07-04 12:49]
2019/08/16 11:35:41:577 INFO Checking whether we need to use a proxy...
2019/08/16 11:35:41:597 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:41:606 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:41:886 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:41:886 INFO Keep on top set to  [keep_on_top=true]
2019/08/16 11:35:41:965 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:41:988 INFO Displaying instant background image
2019/08/16 11:35:42:007 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:008 WARNING Tried to invokeAndWait but couldn't. Going to invokeLater instead [Exception=null]
2019/08/16 11:35:42:015 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:223 INFO Downloading 0 resources [totalBytes=0, maxConcurrent=10]
2019/08/16 11:35:42:238 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:244 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:244 INFO Testing whether proxy is needed, via: http://www.jalview.org/getdown/release/1.8/getdown.txt
2019/08/16 11:35:42:384 INFO No proxy appears to be needed.
2019/08/16 11:35:42:389 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:394 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:395 INFO Downloading 0 resources [totalBytes=0, maxConcurrent=10]
2019/08/16 11:35:42:401 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:432 INFO Able to lock for updates: true
2019/08/16 11:35:42:439 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:443 INFO Verifying application: http://www.jalview.org/getdown/release/1.8/
2019/08/16 11:35:42:444 INFO Version: -1
2019/08/16 11:35:42:444 INFO Class: jalview.bin.Jalview
2019/08/16 11:35:42:467 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:467 INFO Attempting to refetch 'digest.txt' from 'http://www.jalview.org/getdown/release/1.8/digest.txt'.
2019/08/16 11:35:42:480 INFO No signing certs, not verifying digest.txt [path=digest.txt]
2019/08/16 11:35:42:481 INFO Attempting to refetch 'digest2.txt' from 'http://www.jalview.org/getdown/release/1.8/digest2.txt'.
2019/08/16 11:35:42:490 INFO No signing certs, not verifying digest.txt [path=digest2.txt]
2019/08/16 11:35:42:496 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:518 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:521 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:524 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:527 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:530 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:532 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:538 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:540 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:543 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:549 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:552 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:554 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:556 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:559 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:561 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:564 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:566 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:568 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:570 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:573 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:579 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:581 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:583 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:586 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:590 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:592 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:595 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:597 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:600 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:603 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:605 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:608 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:610 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:613 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:616 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:618 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:622 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:626 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:629 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:631 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:634 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:636 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:638 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:641 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:643 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:645 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:647 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:649 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:652 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:658 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:661 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:663 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:665 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:666 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:668 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:670 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:673 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:675 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:677 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:680 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:681 INFO Verified resources [count=60, size=36550k, duration=185ms]
2019/08/16 11:35:42:683 INFO Checking Java version [current=1080202, wantMin=1080000, wantMax=1089999]
2019/08/16 11:35:42:683 INFO vmfile is 'jre.tgz'
vmfile is 'jre.tgz'
2019/08/16 11:35:42:684 INFO Attempting to fetch jvm at http://www.jalview.org/getdown/jre/macos-jre1.8.tgz
Attempting to fetch jvm at http://www.jalview.org/getdown/jre/macos-jre1.8.tgz
2019/08/16 11:35:42:684 INFO Installing 0 downloaded resources:
2019/08/16 11:35:42:684 INFO Install completed.
2019/08/16 11:35:42:686 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]
2019/08/16 11:35:42:690 INFO Didn't find any custom environment variables, not setting any.
2019/08/16 11:35:42:690 INFO Running /Applications/Jalview_real.app/Contents/Resources/app/./jre/Contents/Home/bin/java
  -classpath
  /Applications/Jalview_real.app/Contents/Resources/app/./release/JGoogleAnalytics_0.3.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/Jmol-14.6.4_2016.10.26.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/VARNAv3-93.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/VAqua5-patch.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/activation.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/apache-mime4j-0.6.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/axis.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/biojava-core-4.1.0.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/biojava-ontology-4.1.0.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/commons-codec-1.3.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/commons-compress-1.18.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/commons-discovery.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/commons-logging-1.1.1.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/getdown-core.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/groovy-all-2.4.12-indy.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/htsjdk-2.12.0.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/httpclient-4.0.3.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/httpcore-4.0.1.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/httpmime-4.0.3.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/intervalstore-v1.0.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jabaws-min-client-2.2.0.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jalview.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/java-json.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jaxrpc.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jersey-client-1.19.4.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jersey-core-1.19.4.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jersey-json-1.19.4.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jetty-http-9.2.10.v20150310.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jetty-io-9.2.10.v20150310.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jetty-server-9.2.10.v20150310.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jetty-util-9.2.10.v20150310.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jfreesvg-2.1.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jhall.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/json_simple-1.1.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jsoup-1.8.1.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jsr311-api-1.1.1.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/jswingreader-0.3.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/libquaqua-8.0.jnilib.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/libquaqua64-8.0.jnilib.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/log4j-to-slf4j-2.0-rc2.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/mail.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/miglayout-4.0-swing.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/quaqua-filechooser-only-8.0.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/regex.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/saaj.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/servlet-api-3.1.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/slf4j-api-1.7.7.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/slf4j-log4j12-1.7.7.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/vamsas-client.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/wsdl4j.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/xercesImpl.jar:/Applications/Jalview_real.app/Contents/Resources/app/./release/xml-apis.jar
  -Xdock:icon=/Applications/Jalview_real.app/Contents/Resources/app/./resource/jalview_logos.ico
  -Xdock:name=Jalview
  -Dcom.threerings.getdown=true
  -Dgetdownappdir=/Applications/Jalview_real.app/Contents/Resources/app/.
  -Xmx15461882266
  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:0001648Aug 16, 2019 11:35:44 AM jalview.util.MessageManager <clinit>INFO: Getting messages for lang: en_GBWarning: class ch.randelshofer.quaqua.osx.OSXFile couldn't load library "libquaqua64.dylib". java.lang.UnsatisfiedLinkError: no quaqua64 in java.library.path2019/08/16 11:35:47:570 INFO Max memory set [maxMemHeapArg=-Xmx15461882266]