15:05:10.007 INFO c.a.igb.util.IGBTrustManager - Trusted Certificates:CN=*.bioviz.org; CN=Sectigo RSA Domain Validation Secure Server CA,O=Sectigo Limited,L=Salford,ST=Greater Manchester,C=GB; CN=USERTrust RSA Certification Authority,O=The USERTRUST Network,L=Jersey City,ST=New Jersey,C=US 15:05:10.084 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/chipseq/synonyms.txt 15:05:10.193 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/chipseq/species.txt 15:05:10.196 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server https://bioviz.org/quickload/genome-in-a-bottle/ 15:05:10.727 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from https://bioviz.org/quickload/genome-in-a-bottle/synonyms.txt 15:05:10.865 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: https://bioviz.org/quickload/genome-in-a-bottle/species.txt 15:05:10.941 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/blueberry/ 15:05:11.234 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/blueberry/synonyms.txt 15:05:11.358 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/blueberry/species.txt 15:05:11.379 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server file:/Users/aloraine/src/quickload/ 15:05:11.424 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.HomeAction. But action class com.affymetrix.igb.action.HomeAction exists with same keystroke "ctrl pressed H". Using keystroke with latest action. 15:05:12.165 INFO o.l.i.appstore.IgbAppServerLauncher - setPlugingManagerService START 15:05:12.165 INFO o.l.i.appstore.IgbAppServerLauncher - setPluginManagerService DONE 15:05:12.165 INFO o.l.i.appstore.IgbAppServerLauncher - activate START 15:05:12.165 INFO o.l.i.appstore.IgbAppServerLauncher - org.lorainelab.igb.plugin.manager.service.impl.PluginManagerServiceImpl@22fd7a95 15:05:12.166 INFO o.l.i.appstore.IgbAppServerLauncher - activate DONE 15:05:12.169 INFO o.l.i.appstore.IgbAppServerLauncher - Started REST endpoint. 15:05:12.268 INFO c.a.i.b.action.BookmarkActionManager - Loading bookmarks from file /Users/aloraine/.igb/bookmarks.html 15:05:12.269 INFO c.a.i.b.action.BookmarkActionManager - Saving bookmarks to file /Users/aloraine/.igb/bookmarks.html~ 15:05:12.405 INFO com.affymetrix.igb.Activator - IGB Started 15:05:12.484 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.framework 15:05:12.484 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.sun.xml.fastinfoset.FastInfoset 15:05:12.484 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common 15:05:12.484 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: appstore 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bam 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bed 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: BigWig 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache-api 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-codec 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-compress 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-csv 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-fileupload 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-io 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.jexl 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.lang3 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.logging 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.pool 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: console-tab 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: context-menu-service 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.external-sort 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: externalView 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava.failureaccess 15:05:12.485 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.feedback 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: frameManager 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: genometry 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.genotyping 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.genoviz 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.gson 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: null 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-javafx-util 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-preferences 15:05:12.486 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: image-exporter 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.sun.istack.commons-runtime 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: jakarta.activation-api 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: jakarta.xml.bind-api 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.glassfish.jaxb.core 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.glassfish.jaxb.runtime 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.jidesoft.ultimate.jakarta 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keybinding-registry 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.classic 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.core 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.logging-config 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.narrowpeak 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.bundlerepository 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.configadmin 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.eventadmin 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: null 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.jetty 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.servlet-api 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.scr 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.webconsole 15:05:12.487 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.menu.api 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.service.component 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.service.log 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.util.function 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.util.promise 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.glassfish.hk2.osgi-resource-locator 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.plugins-manager 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: quickload 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchView 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: session-manager 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: slf4j.api 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: survey 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: synonym-lookup 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: track-operations-panel 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: null 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ucsc-rest-api-service 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: update 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: weblinks 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: window-service 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.tukaani.xz 15:05:12.488 [main] INFO com.affymetrix.main.OSGiHandler - OSGi is started with org.apache.felix.framework version 7.0.5 15:05:16.806 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded RefSeq Curated in 632.9 ms 15:05:39.274 INFO c.a.igb.util.IGBTrustManager - Trusted Certificates:CN=collections.ac2it.arvadosapi.com; CN=R11,O=Let's Encrypt,C=US 15:05:56.102 INFO org.lorainelab.igb.cram.CRAM - Initialising CRAM parser 15:05:56.631 INFO c.a.igb.util.IGBTrustManager - Trusted Certificates:CN=*.cyverse.org; CN=Go Daddy Secure Certificate Authority - G2,OU=http://certs.godaddy.com/repository/,O=GoDaddy.com\, Inc.,L=Scottsdale,ST=Arizona,C=US; CN=Go Daddy Root Certificate Authority - G2,O=GoDaddy.com\, Inc.,L=Scottsdale,ST=Arizona,C=US; OU=Go Daddy Class 2 Certification Authority,O=The Go Daddy Group\, Inc.,C=US 15:05:57.882 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,092,019 - 79,130,151 from Your server name file:/Users/aloraine/src/quickload/ 15:05:58.337 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,130,004 - 79,169,301 from Your server name file:/Users/aloraine/src/quickload/ 15:05:58.617 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,169,174 - 79,209,467 from Your server name file:/Users/aloraine/src/quickload/ 15:05:58.856 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,209,318 - 79,249,197 from Your server name file:/Users/aloraine/src/quickload/ 15:05:59.084 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,249,048 - 79,287,281 from Your server name file:/Users/aloraine/src/quickload/ 15:05:59.337 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,287,139 - 79,326,304 from Your server name file:/Users/aloraine/src/quickload/ 15:05:59.575 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,326,159 - 79,364,187 from Your server name file:/Users/aloraine/src/quickload/ 15:05:59.802 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,364,037 - 79,404,349 from Your server name file:/Users/aloraine/src/quickload/ 15:06:00.027 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,404,200 - 79,444,280 from Your server name file:/Users/aloraine/src/quickload/ 15:06:00.258 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,444,135 - 79,483,584 from Your server name file:/Users/aloraine/src/quickload/ 15:06:00.483 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,483,442 - 79,523,619 from Your server name file:/Users/aloraine/src/quickload/ 15:06:00.718 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,523,470 - 79,563,087 from Your server name file:/Users/aloraine/src/quickload/ 15:06:00.943 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,562,938 - 79,605,261 from Your server name file:/Users/aloraine/src/quickload/ 15:06:01.175 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 79,605,112 - 79,645,137 from Your server name file:/Users/aloraine/src/quickload/ Jan 06, 2025 3:06:10 PM com.affymetrix.genometry.symloader.TwoBitNew getRegionResidues WARNING: Seq chrEBV not present file:/Users/aloraine/src/quickload/H_sapiens_Dec_2013/H_sapiens_Dec_2013.2bit Jan 06, 2025 3:06:11 PM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException SEVERE: java.lang.IllegalArgumentException: Failure getting reference bases for sequence chrEBV java.lang.Exception: java.lang.IllegalArgumentException: Failure getting reference bases for sequence chrEBV at org.lorainelab.igb.cram.CRAM.parse(CRAM.java:151) at org.lorainelab.igb.bam.XAM.getRegion(XAM.java:124) at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getRegion(QuickLoadSymLoader.java:287) at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:164) at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:139) at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:119) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:757) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:699) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:694) at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:305) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317) at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:342) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1583) Caused by: java.lang.IllegalArgumentException: Failure getting reference bases for sequence chrEBV at htsjdk.samtools.cram.build.CRAMReferenceRegion.fetchReferenceBasesByRegion(CRAMReferenceRegion.java:172) at htsjdk.samtools.cram.build.CRAMReferenceRegion.fetchReferenceBasesByRegion(CRAMReferenceRegion.java:192) at htsjdk.samtools.cram.structure.Slice.normalizeCRAMRecords(Slice.java:450) at htsjdk.samtools.cram.structure.Container.getSAMRecords(Container.java:322) at htsjdk.samtools.CRAMIterator.nextContainer(CRAMIterator.java:112) at htsjdk.samtools.CRAMIterator.hasNext(CRAMIterator.java:204) at htsjdk.samtools.CRAMFileReader$CRAMIntervalIteratorBase.getNextRecord(CRAMFileReader.java:589) at htsjdk.samtools.CRAMFileReader$CRAMIntervalIteratorBase.initializeIterator(CRAMFileReader.java:562) at htsjdk.samtools.CRAMFileReader$CRAMIntervalIterator.<init>(CRAMFileReader.java:620) at htsjdk.samtools.CRAMFileReader$CRAMIntervalIterator.<init>(CRAMFileReader.java:615) at htsjdk.samtools.CRAMFileReader.query(CRAMFileReader.java:487) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:550) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:555) at org.lorainelab.igb.cram.CRAM.parse(CRAM.java:131) ... 15 more