2020/06/18 19:27:37:489 INFO Using appdir from command line: /home/psgendb/BIRCHDEV/java/Jalview/ 2020/06/18 19:27:37:493 INFO Using appid from command line: jalview 2020/06/18 19:27:37:493 INFO Starting ... 2020/06/18 19:27:37:501 INFO ------------------ VM Info ------------------ 2020/06/18 19:27:37:502 INFO -- OS Name: Linux 2020/06/18 19:27:37:502 INFO -- OS Arch: amd64 2020/06/18 19:27:37:502 INFO -- OS Vers: 3.10.0-1127.8.2.el7.x86_64 2020/06/18 19:27:37:502 INFO -- Java Vers: 1.8.0_242 2020/06/18 19:27:37:503 INFO -- Java Home: /home/psgendb/BIRCHDEV/java/Jalview2.11.1.0/jre 2020/06/18 19:27:37:510 INFO -- Install4j Vers: null 2020/06/18 19:27:37:510 INFO -- Install4j Template Vers: 2.11.1.0_F10e9b8be_C30119dce1 2020/06/18 19:27:37:510 INFO -- User Name: psgendb 2020/06/18 19:27:37:511 INFO -- User Home: /home/psgendb 2020/06/18 19:27:37:511 INFO -- Cur dir: /home/psgendb/temp/clustalo 2020/06/18 19:27:37:511 INFO -- Launcher version: 1.8.3-1.2.4_JVL 2020/06/18 19:27:37:512 INFO -- startupFilesParameterString: 2020/06/18 19:27:37:512 INFO --------------------------------------------- 2020/06/18 19:27:37:626 INFO Getdown starting [version=1.8.3-1.2.4_JVL, built=2020-04-02 14:45] 2020/06/18 19:27:37:633 INFO Checking whether we need to use a proxy... 2020/06/18 19:27:37:975 INFO Keep on top set to [keep_on_top=true] 2020/06/18 19:27:38:069 INFO Displaying instant background image 2020/06/18 19:27:38:084 WARNING Tried to invokeAndWait but couldn't. Going to invokeLater instead [Exception=null] 2020/06/18 19:27:38:281 INFO Downloading 0 resources [totalBytes=0, maxConcurrent=10] 2020/06/18 19:27:38:287 INFO Testing whether proxy is needed, via: https://www.jalview.org/getdown/release/1.8/getdown.txt 2020/06/18 19:27:39:255 INFO No proxy appears to be needed. 2020/06/18 19:27:39:265 INFO Downloading 0 resources [totalBytes=0, maxConcurrent=10] 2020/06/18 19:27:39:270 INFO Able to lock for updates: true 2020/06/18 19:27:39:271 INFO Verifying application: https://www.jalview.org/getdown/release/1.8/ 2020/06/18 19:27:39:271 INFO Version: -1 2020/06/18 19:27:39:271 INFO Class: jalview.bin.Jalview 2020/06/18 19:27:39:274 INFO Attempting to refetch 'digest.txt' from 'https://www.jalview.org/getdown/release/1.8/digest.txt'. 2020/06/18 19:27:39:410 INFO No signing certs, not verifying digest.txt [path=digest.txt] 2020/06/18 19:27:39:412 INFO Attempting to refetch 'digest2.txt' from 'https://www.jalview.org/getdown/release/1.8/digest2.txt'. 2020/06/18 19:27:39:540 INFO No signing certs, not verifying digest.txt [path=digest2.txt] 2020/06/18 19:27:39:627 INFO Verified resources [count=59, size=38679k, duration=81ms] 2020/06/18 19:27:39:629 INFO Checking Java version [current=1080242, wantMin=1080000, wantMax=1089999] 2020/06/18 19:27:39:629 INFO Installing 0 downloaded resources: 2020/06/18 19:27:39:630 INFO Install completed. 2020/06/18 19:27:39:635 INFO TRYING TO PARSE URL '-open' 2020/06/18 19:27:39:638 INFO Didn't find any custom environment variables, not setting any. 2020/06/18 19:27:39:638 INFO Running /home/psgendb/BIRCHDEV/java/Jalview/jre/bin/java -classpath /home/psgendb/BIRCHDEV/java/Jalview/release/JGoogleAnalytics_0.3.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/Jmol-14.6.4_2016.10.26.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/VARNAv3-93.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/VAqua5-patch.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/activation.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/apache-mime4j-0.6.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/axis.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/biojava-core-4.1.0.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/biojava-ontology-4.1.0.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/commons-codec-1.3.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/commons-discovery.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/commons-logging-1.1.1.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/getdown-core.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/groovy-all-2.4.12-indy.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/htsjdk-2.12.0.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/httpclient-4.0.3.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/httpcore-4.0.1.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/httpmime-4.0.3.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/intervalstore-v1.0.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jabaws-min-client-2.2.0.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jalview.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/java-json.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jaxrpc.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jersey-client-1.19.4.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jersey-core-1.19.4.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jersey-json-1.19.4.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jetty-http-9.2.10.v20150310.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jetty-io-9.2.10.v20150310.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jetty-server-9.2.10.v20150310.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jetty-util-9.2.10.v20150310.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jfreesvg-2.1.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jhall.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/json_simple-1.1.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jsoup-1.8.1.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jsr311-api-1.1.1.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/jswingreader-0.3.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/libquaqua-8.0.jnilib.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/libquaqua64-8.0.jnilib.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/log4j-to-slf4j-2.0-rc2.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/mail.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/miglayout-4.0-swing.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/quaqua-filechooser-only-8.0.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/regex.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/saaj.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/servlet-api-3.1.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/slf4j-api-1.7.7.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/slf4j-log4j12-1.7.7.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/vamsas-client.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/wsdl4j.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/xercesImpl.jar:/home/psgendb/BIRCHDEV/java/Jalview/release/xml-apis.jar -Dcom.threerings.getdown=true -Dsys.install4jVersion=8.0.5 -Dinstaller_template_version=2.11.1.0_F10e9b8be_C30119dce1 -Dlauncher_version=1.8.3-1.2.4_JVL -Dgetdownappdir=/home/psgendb/BIRCHDEV/java/Jalview -Xmx34359738368 jalview.bin.Jalview -open /home/psgendb/temp/clustalo/bio256772891339785590.tmp.fsa 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:0001648Jun 18, 2020 7:27:40 PM jalview.util.MessageManager INFO: Getting messages for lang: en_USJun 18, 2020 7:27:41 PM compbio.ws.client.Jws2Client connectToRegistryINFO: Connected to RegistryWS successfully!Jun 18, 2020 7:27:42 PM compbio.ws.client.Jws2Client connectINFO: Connected successfully!