simple	23-Jan-2025 15:24:47	Build Jalview Builds - Getdown Plan Channel - Default Job #354 (JB-GPC-JOB1-354) started building on agent Default Agent
simple	23-Jan-2025 15:24:47	
simple	23-Jan-2025 15:24:47	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1
simple	23-Jan-2025 15:24:47	Executing build Jalview Builds - Getdown Plan Channel - Default Job #354 (JB-GPC-JOB1-354)
simple	23-Jan-2025 15:24:47	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	23-Jan-2025 15:24:47	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1
simple	23-Jan-2025 15:24:47	Updating source code to revision: 1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a
simple	23-Jan-2025 15:24:47	Fetching 'refs/heads/develop' from 'http://source.jalview.org/git/jalview.git'.
simple	23-Jan-2025 15:24:48	Checking out revision 1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a.
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Pre_R29_develop does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/RNAalifold does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Release_2_4_branch does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/VamJalview does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object!
simple	23-Jan-2025 15:24:48	error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-1499 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-2103 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/j2s/develop does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/j2s/develop-bh does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/j2s/develop-jim does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/j2s/develop-toc does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/jalview-headless does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:49	error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/clinvar does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/phyre2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/jim does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/kira does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/koen does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/mungo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/phyre does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/thomas does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/toch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/vamsasDemo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Pre_R29_develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/RNAalifold does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_4_branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/VamJalview does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1499 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2103 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-bh does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-jim does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-toc does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/jalview-headless does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/clinvar does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/phyre2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/jim does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/kira does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/koen does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/mungo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/phyre does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/thomas does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/toch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/vamsasDemo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Pre_R29_develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/RNAalifold does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_4_branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/VamJalview does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1499 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2103 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-bh does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-jim does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-toc does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/jalview-headless does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/clinvar does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/phyre2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/jim does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/kira does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/koen does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/mungo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/phyre does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/thomas does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/toch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/vamsasDemo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Pre_R29_develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/RNAalifold does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_4_branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/VamJalview does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1499 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2103 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-bh does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-jim does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/j2s/develop-toc does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/jalview-headless does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/clinvar does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/phyre2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/jim does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/kira does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/koen does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/mungo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/phyre does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/thomas does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/spikes/toch does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/remotes/origin/vamsasDemo does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	23-Jan-2025 15:24:50	Already on 'develop'
simple	23-Jan-2025 15:24:50	Updated source code to revision: 1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a
simple	23-Jan-2025 15:24:50	Finished task 'Checkout Default Repository' with result: Success
simple	23-Jan-2025 15:24:50	Running pre-build action: VCS Version Collector
simple	23-Jan-2025 15:24:50	Running pre-build action: Artifactory Release Staging
command	23-Jan-2025 15:24:50	Substituting variable: ${bamboo.planKey} with JB-GPC
simple	23-Jan-2025 15:24:50	Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	23-Jan-2025 15:24:50	Bamboo Artifactory Plugin version: 2.6.2
command	23-Jan-2025 15:24:50	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - Default Job #354 (JB-GPC-JOB1-354)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC clean shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_dependency_parent_0=JB-GDB-702\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_9175083_git_branch=develop\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC-JOB1-354\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GPC-JOB1\nbamboo_shortPlanName=Getdown Plan Channel\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=354\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_9175083_previous_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC-JOB1-354\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel\nbamboo_shortPlanKey=GPC\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_buildTimeStamp=2025-01-23T15:22:06.370Z\nbamboo_repository_previous_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_planRepository_previousRevision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_repository_9175083_name=Jalview Git\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GPC-JOB1-354\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_repository_9175083_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=develop\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\nbamboo_repository_9175083_branch_name=develop\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_9175083_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-8978517\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1\nbamboo_planKey=JB-GPC\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_9175083_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	23-Jan-2025 15:24:52	
build	23-Jan-2025 15:24:52	> Configure project :
build	23-Jan-2025 15:24:52	Using properties from file './utils/channels/default/channel_gradle.properties'
build	23-Jan-2025 15:24:52	JALVIEW_VERSION is set to '2.11.4.2'
build	23-Jan-2025 15:24:52	HEADLESS BUILD
build	23-Jan-2025 15:24:52	J2S ENABLED
build	23-Jan-2025 15:24:52	Using a BUILD profile.
build	23-Jan-2025 15:24:52	eclipseDir exists
build	23-Jan-2025 15:24:52	
build	23-Jan-2025 15:24:52	> Task :clean
build	23-Jan-2025 15:24:52	> Task :cleanPackageDir
build	23-Jan-2025 15:24:53	> Task :copyHelp
build	23-Jan-2025 15:24:57	> Task :buildIndices
build	23-Jan-2025 15:24:57	> Task :copyResources
build	23-Jan-2025 15:24:57	> Task :copyChannelResources
build	23-Jan-2025 15:24:57	
build	23-Jan-2025 15:24:57	> Task :createBuildProperties
build	23-Jan-2025 15:24:57	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	23-Jan-2025 15:24:57	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:24:57	
build	23-Jan-2025 15:24:57	> Task :buildResources
build	23-Jan-2025 15:24:57	> Task :copyDocs
build	23-Jan-2025 15:24:57	
build	23-Jan-2025 15:24:57	> Task :convertMdFiles
build	23-Jan-2025 15:24:57	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	23-Jan-2025 15:24:57	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	23-Jan-2025 15:24:57	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	23-Jan-2025 15:24:57	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/building.html
build	23-Jan-2025 15:24:57	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	23-Jan-2025 15:24:57	
build	23-Jan-2025 15:24:57	> Task :releasesTemplates
build	23-Jan-2025 15:24:57	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	23-Jan-2025 15:24:57	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:24:57	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:24:57	Stripping rc/test/etc for 2_11_4_2
build	23-Jan-2025 15:24:57	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_2.md
build	23-Jan-2025 15:24:57	
build	23-Jan-2025 15:24:57	> Task :prepare
build	23-Jan-2025 15:24:59	
build	23-Jan-2025 15:24:59	> Task :compileJava
build	23-Jan-2025 15:24:59	Setting target compatibility to 11
error	23-Jan-2025 15:25:08	Note: Some input files use or override a deprecated API.
error	23-Jan-2025 15:25:08	Note: Recompile with -Xlint:deprecation for details.
error	23-Jan-2025 15:25:08	Note: Some input files use unchecked or unsafe operations.
error	23-Jan-2025 15:25:08	Note: Recompile with -Xlint:unchecked for details.
build	23-Jan-2025 15:25:08	
build	23-Jan-2025 15:25:08	> Task :processResources
build	23-Jan-2025 15:25:08	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	23-Jan-2025 15:25:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:25:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:25:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:25:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:25:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:25:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:25:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:25:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:25:08	
build	23-Jan-2025 15:25:08	> Task :classes
build	23-Jan-2025 15:25:10	
build	23-Jan-2025 15:25:10	> Task :compileLinkCheck
build	23-Jan-2025 15:25:10	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	23-Jan-2025 15:25:10	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:25:10	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:25:12	
build	23-Jan-2025 15:25:12	> Task :linkCheck
build	23-Jan-2025 15:25:12	Checking help file links
build	23-Jan-2025 15:27:17	
build	23-Jan-2025 15:27:17	Results:
build	23-Jan-2025 15:27:17	159 distinct help targets
build	23-Jan-2025 15:27:17	159 help mappings
build	23-Jan-2025 15:27:17	0 invalid targets
build	23-Jan-2025 15:27:17	32 unused targets
build	23-Jan-2025 15:27:17	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	23-Jan-2025 15:27:17	    overviewprefs: html/features/preferences.html#overview
build	23-Jan-2025 15:27:17	    cdnafeatures: html/features/codingfeatures.html
build	23-Jan-2025 15:27:17	    startupprefs: html/features/preferences.html#startup
build	23-Jan-2025 15:27:17	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	23-Jan-2025 15:27:17	    io.modellerpir: html/io/modellerpir.html
build	23-Jan-2025 15:27:17	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	23-Jan-2025 15:27:17	    pdbmcviewer: html/features/pdbviewer.html
build	23-Jan-2025 15:27:17	    workingwithpae: html/features/paematrices.html
build	23-Jan-2025 15:27:17	    groovy.colours: html/features/groovy.html#groovyColours
build	23-Jan-2025 15:27:17	    seqmappings: html/features/seqmappings.html
build	23-Jan-2025 15:27:17	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	23-Jan-2025 15:27:17	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	23-Jan-2025 15:27:17	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	23-Jan-2025 15:27:17	    search: html/features/search.html
build	23-Jan-2025 15:27:17	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	23-Jan-2025 15:27:17	    alformats: html/io/fileformats.html
build	23-Jan-2025 15:27:17	    strucprefs: html/features/preferences.html#structure
build	23-Jan-2025 15:27:17	    siftsmapping: html/features/siftsmapping.html
build	23-Jan-2025 15:27:17	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	23-Jan-2025 15:27:17	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	23-Jan-2025 15:27:17	    newkeys: html/features/newkeystrokes.html
build	23-Jan-2025 15:27:17	    importvcf.attribs: html/features/importvcf.html#attribs
build	23-Jan-2025 15:27:17	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	23-Jan-2025 15:27:17	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	23-Jan-2025 15:27:17	    jalarchive: html/features/jalarchive.html
build	23-Jan-2025 15:27:17	    newsreader: html/webServices/newsreader.html
build	23-Jan-2025 15:27:17	    jalviewcltool: html/features/commandline.html#script
build	23-Jan-2025 15:27:17	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	23-Jan-2025 15:27:17	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	23-Jan-2025 15:27:17	    paematrixformat: html/io/paematrixformat.html
build	23-Jan-2025 15:27:17	    overview: html/features/overview.html
build	23-Jan-2025 15:27:17	0 invalid map urls
build	23-Jan-2025 15:27:17	0 invalid image attributes
build	23-Jan-2025 15:27:17	506 internal href links (110 with anchors)
build	23-Jan-2025 15:27:17	0 invalid internal href links
build	23-Jan-2025 15:27:17	0 invalid internal anchor links
build	23-Jan-2025 15:27:17	112 external href links
build	23-Jan-2025 15:27:17	External links not verified as internet not available
build	23-Jan-2025 15:27:17	*** Success ***
build	23-Jan-2025 15:27:18	
build	23-Jan-2025 15:27:18	> Task :jar
build	23-Jan-2025 15:27:20	> Task :syncJars
build	23-Jan-2025 15:27:20	> Task :makeDist
build	23-Jan-2025 15:27:31	> Task :shadowJar
build	23-Jan-2025 15:27:31	
build	23-Jan-2025 15:27:31	> Task :getdownImagesCopy
build	23-Jan-2025 15:27:31	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	23-Jan-2025 15:27:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/utils/channels/default/images'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:31	
build	23-Jan-2025 15:27:31	> Task :getdownImagesProcess
build	23-Jan-2025 15:27:31	> Task :getdownImages
build	23-Jan-2025 15:27:32	> Task :getdownWebsiteBuild
build	23-Jan-2025 15:27:33	
build	23-Jan-2025 15:27:33	> Task :getdownDigest
build	23-Jan-2025 15:27:33	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build	23-Jan-2025 15:27:33	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	23-Jan-2025 15:27:33	
build	23-Jan-2025 15:27:33	> Task :getdown
build	23-Jan-2025 15:27:33	
build	23-Jan-2025 15:27:33	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	23-Jan-2025 15:27:33	
build	23-Jan-2025 15:27:33	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	23-Jan-2025 15:27:33	
error	23-Jan-2025 15:27:33	2025/01/23 15:27:32:220 WARNING Starting without install4j classes
error	23-Jan-2025 15:27:33	2025/01/23 15:27:32:786 WARNING Starting without install4j classes
build	23-Jan-2025 15:27:33	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	23-Jan-2025 15:27:33	
build	23-Jan-2025 15:27:33	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	23-Jan-2025 15:27:33	Please consult deprecation warnings for more details.
build	23-Jan-2025 15:27:33	
build	23-Jan-2025 15:27:33	BUILD SUCCESSFUL in 2m 42s
build	23-Jan-2025 15:27:33	22 actionable tasks: 22 executed
simple	23-Jan-2025 15:27:33	Finished task 'Jalview distribution for Java 11' with result: Success
command	23-Jan-2025 15:27:33	Substituting variable: ${bamboo.planKey} with JB-GPC
simple	23-Jan-2025 15:27:33	Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	23-Jan-2025 15:27:33	Bamboo Artifactory Plugin version: 2.6.2
command	23-Jan-2025 15:27:33	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - Default Job #354 (JB-GPC-JOB1-354)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PCHANNEL=BUILD -PJAVA_VERSION=1.8 -Pbamboo_planKey=JB-GPC shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_dependency_parent_0=JB-GDB-702\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_9175083_git_branch=develop\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC-JOB1-354\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GPC-JOB1\nbamboo_shortPlanName=Getdown Plan Channel\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=354\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_9175083_previous_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC-JOB1-354\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel\nbamboo_shortPlanKey=GPC\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_buildTimeStamp=2025-01-23T15:22:06.370Z\nbamboo_repository_previous_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_planRepository_previousRevision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_repository_9175083_name=Jalview Git\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GPC-JOB1-354\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_repository_9175083_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC clean shadowJar getdown\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=develop\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\nbamboo_repository_9175083_branch_name=develop\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_9175083_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-8978517\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1\nbamboo_planKey=JB-GPC\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_9175083_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	23-Jan-2025 15:27:34	
build	23-Jan-2025 15:27:34	> Configure project :
build	23-Jan-2025 15:27:34	Using properties from file './utils/channels/default/channel_gradle.properties'
build	23-Jan-2025 15:27:34	JALVIEW_VERSION is set to '2.11.4.2'
build	23-Jan-2025 15:27:34	HEADLESS BUILD
build	23-Jan-2025 15:27:34	J2S ENABLED
build	23-Jan-2025 15:27:34	Using a BUILD profile.
build	23-Jan-2025 15:27:34	eclipseDir exists
build	23-Jan-2025 15:27:34	
build	23-Jan-2025 15:27:34	> Task :copyHelp UP-TO-DATE
build	23-Jan-2025 15:27:36	> Task :buildIndices
build	23-Jan-2025 15:27:36	> Task :copyResources
build	23-Jan-2025 15:27:36	> Task :copyChannelResources UP-TO-DATE
build	23-Jan-2025 15:27:36	
build	23-Jan-2025 15:27:36	> Task :createBuildProperties
build	23-Jan-2025 15:27:36	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	23-Jan-2025 15:27:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:36	
build	23-Jan-2025 15:27:36	> Task :buildResources
build	23-Jan-2025 15:27:36	> Task :copyDocs
build	23-Jan-2025 15:27:36	
build	23-Jan-2025 15:27:36	> Task :convertMdFiles
build	23-Jan-2025 15:27:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	23-Jan-2025 15:27:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	23-Jan-2025 15:27:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	23-Jan-2025 15:27:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/building.html
build	23-Jan-2025 15:27:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	23-Jan-2025 15:27:36	
build	23-Jan-2025 15:27:36	> Task :releasesTemplates
build	23-Jan-2025 15:27:36	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	23-Jan-2025 15:27:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:36	Stripping rc/test/etc for 2_11_4_2
build	23-Jan-2025 15:27:36	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_2.md
build	23-Jan-2025 15:27:36	
build	23-Jan-2025 15:27:36	> Task :prepare
build	23-Jan-2025 15:27:38	
build	23-Jan-2025 15:27:38	> Task :compileJava
build	23-Jan-2025 15:27:38	Setting target compatibility to 1.8
error	23-Jan-2025 15:27:43	Note: Some input files use or override a deprecated API.
error	23-Jan-2025 15:27:43	Note: Recompile with -Xlint:deprecation for details.
error	23-Jan-2025 15:27:43	Note: Some input files use unchecked or unsafe operations.
error	23-Jan-2025 15:27:43	Note: Recompile with -Xlint:unchecked for details.
build	23-Jan-2025 15:27:47	
build	23-Jan-2025 15:27:47	> Task :processResources
build	23-Jan-2025 15:27:47	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	23-Jan-2025 15:27:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:47	
build	23-Jan-2025 15:27:47	> Task :classes
build	23-Jan-2025 15:27:47	> Task :cleanPackageDir
build	23-Jan-2025 15:27:48	
build	23-Jan-2025 15:27:48	> Task :compileLinkCheck
build	23-Jan-2025 15:27:48	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	23-Jan-2025 15:27:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:27:50	
build	23-Jan-2025 15:27:50	> Task :linkCheck
build	23-Jan-2025 15:27:50	Checking help file links
build	23-Jan-2025 15:29:56	
build	23-Jan-2025 15:29:56	Results:
build	23-Jan-2025 15:29:56	159 distinct help targets
build	23-Jan-2025 15:29:56	159 help mappings
build	23-Jan-2025 15:29:56	0 invalid targets
build	23-Jan-2025 15:29:56	32 unused targets
build	23-Jan-2025 15:29:56	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	23-Jan-2025 15:29:56	    overviewprefs: html/features/preferences.html#overview
build	23-Jan-2025 15:29:56	    cdnafeatures: html/features/codingfeatures.html
build	23-Jan-2025 15:29:56	    startupprefs: html/features/preferences.html#startup
build	23-Jan-2025 15:29:56	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	23-Jan-2025 15:29:56	    io.modellerpir: html/io/modellerpir.html
build	23-Jan-2025 15:29:56	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	23-Jan-2025 15:29:56	    pdbmcviewer: html/features/pdbviewer.html
build	23-Jan-2025 15:29:56	    workingwithpae: html/features/paematrices.html
build	23-Jan-2025 15:29:56	    groovy.colours: html/features/groovy.html#groovyColours
build	23-Jan-2025 15:29:56	    seqmappings: html/features/seqmappings.html
build	23-Jan-2025 15:29:56	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	23-Jan-2025 15:29:56	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	23-Jan-2025 15:29:56	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	23-Jan-2025 15:29:56	    search: html/features/search.html
build	23-Jan-2025 15:29:56	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	23-Jan-2025 15:29:56	    alformats: html/io/fileformats.html
build	23-Jan-2025 15:29:56	    strucprefs: html/features/preferences.html#structure
build	23-Jan-2025 15:29:56	    siftsmapping: html/features/siftsmapping.html
build	23-Jan-2025 15:29:56	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	23-Jan-2025 15:29:56	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	23-Jan-2025 15:29:56	    newkeys: html/features/newkeystrokes.html
build	23-Jan-2025 15:29:56	    importvcf.attribs: html/features/importvcf.html#attribs
build	23-Jan-2025 15:29:56	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	23-Jan-2025 15:29:56	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	23-Jan-2025 15:29:56	    jalarchive: html/features/jalarchive.html
build	23-Jan-2025 15:29:56	    newsreader: html/webServices/newsreader.html
build	23-Jan-2025 15:29:56	    jalviewcltool: html/features/commandline.html#script
build	23-Jan-2025 15:29:56	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	23-Jan-2025 15:29:56	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	23-Jan-2025 15:29:56	    paematrixformat: html/io/paematrixformat.html
build	23-Jan-2025 15:29:56	    overview: html/features/overview.html
build	23-Jan-2025 15:29:56	0 invalid map urls
build	23-Jan-2025 15:29:56	0 invalid image attributes
build	23-Jan-2025 15:29:56	506 internal href links (110 with anchors)
build	23-Jan-2025 15:29:56	0 invalid internal href links
build	23-Jan-2025 15:29:56	0 invalid internal anchor links
build	23-Jan-2025 15:29:56	112 external href links
build	23-Jan-2025 15:29:56	External links not verified as internet not available
build	23-Jan-2025 15:29:56	*** Success ***
build	23-Jan-2025 15:29:57	
build	23-Jan-2025 15:29:57	> Task :jar
build	23-Jan-2025 15:29:59	> Task :syncJars
build	23-Jan-2025 15:29:59	> Task :makeDist
build	23-Jan-2025 15:30:06	> Task :shadowJar
build	23-Jan-2025 15:30:06	
build	23-Jan-2025 15:30:06	> Task :getdownImagesCopy
build	23-Jan-2025 15:30:06	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	23-Jan-2025 15:30:06	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/utils/channels/default/images'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	23-Jan-2025 15:30:06	
build	23-Jan-2025 15:30:06	> Task :getdownImagesProcess
build	23-Jan-2025 15:30:06	> Task :getdownImages
build	23-Jan-2025 15:30:06	> Task :getdownWebsiteBuild
build	23-Jan-2025 15:30:08	
build	23-Jan-2025 15:30:08	> Task :getdownDigest
build	23-Jan-2025 15:30:08	Generating digest file './build/website/docroot/getdown/default/1.8/digest.txt'...
error	23-Jan-2025 15:30:08	2025/01/23 15:30:07:073 WARNING Starting without install4j classes
build	23-Jan-2025 15:30:08	Generating digest file './build/website/docroot/getdown/default/1.8/digest2.txt'...
error	23-Jan-2025 15:30:08	2025/01/23 15:30:07:562 WARNING Starting without install4j classes
build	23-Jan-2025 15:30:08	
build	23-Jan-2025 15:30:08	> Task :getdown
build	23-Jan-2025 15:30:08	
build	23-Jan-2025 15:30:08	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	23-Jan-2025 15:30:08	
build	23-Jan-2025 15:30:08	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	23-Jan-2025 15:30:08	
build	23-Jan-2025 15:30:08	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	23-Jan-2025 15:30:08	
build	23-Jan-2025 15:30:08	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	23-Jan-2025 15:30:08	Please consult deprecation warnings for more details.
build	23-Jan-2025 15:30:08	
build	23-Jan-2025 15:30:08	BUILD SUCCESSFUL in 2m 34s
build	23-Jan-2025 15:30:08	21 actionable tasks: 19 executed, 2 up-to-date
simple	23-Jan-2025 15:30:08	Finished task 'Jalview distribution for Java 8' with result: Success
simple	23-Jan-2025 15:30:08	Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled
simple	23-Jan-2025 15:30:08	Running post build plugin 'NCover Results Collector'
simple	23-Jan-2025 15:30:08	Running post build plugin 'Artifact Copier'
simple	23-Jan-2025 15:30:08	Publishing an artifact: Jalview executables
simple	23-Jan-2025 15:30:08	Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 141.1 ms
simple	23-Jan-2025 15:30:08	Publishing an artifact: install4j installers
error	23-Jan-2025 15:30:08	Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/install4j does not exist.
simple	23-Jan-2025 15:30:08	The artifact hasn't been successfully published after 1.540 ms
simple	23-Jan-2025 15:30:08	Publishing an artifact: getdown-channel
simple	23-Jan-2025 15:30:12	Finished publishing of artifact Shared artifact: [getdown-channel], pattern: [**/*] anchored at: [getdown/website] in 3.426 s
simple	23-Jan-2025 15:30:12	Publishing an artifact: Jalview getdown launcher
simple	23-Jan-2025 15:30:12	Finished publishing of artifact Shared artifact: [Jalview getdown launcher], pattern: [**/*] anchored at: [getdown/files] in 48.09 ms
simple	23-Jan-2025 15:30:12	Publishing an artifact: getdown build for website
simple	23-Jan-2025 15:30:12	Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 214.0 ms
simple	23-Jan-2025 15:30:12	Publishing an artifact: getdown build for archive
error	23-Jan-2025 15:30:12	Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/website/docroot/old does not exist.
simple	23-Jan-2025 15:30:12	The artifact hasn't been successfully published after 101.2 μs
simple	23-Jan-2025 15:30:12	Running post build plugin 'Artifactory Release Management Staging'
simple	23-Jan-2025 15:30:12	Running post build plugin 'Artifactory Build Info Copier'
simple	23-Jan-2025 15:30:12	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	23-Jan-2025 15:30:12	Running post build plugin 'npm Cache Cleanup'
simple	23-Jan-2025 15:30:12	Running post build plugin 'Clover Results Collector'
simple	23-Jan-2025 15:30:12	Running post build plugin 'Docker Container Cleanup'
simple	23-Jan-2025 15:30:12	Finalising the build...
simple	23-Jan-2025 15:30:12	Stopping timer.
simple	23-Jan-2025 15:30:12	Build JB-GPC-JOB1-354 completed.
simple	23-Jan-2025 15:30:12	Running on server: post build plugin 'NCover Results Collector'
simple	23-Jan-2025 15:30:12	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	23-Jan-2025 15:30:12	Running on server: post build plugin 'Clover Delta Calculator'
simple	23-Jan-2025 15:30:12	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	23-Jan-2025 15:30:12	All post build plugins have finished
simple	23-Jan-2025 15:30:12	Generating build results summary...
simple	23-Jan-2025 15:30:12	Saving build results to disk...
simple	23-Jan-2025 15:30:12	Logging substituted variables...
simple	23-Jan-2025 15:30:12	Indexing build results...
simple	23-Jan-2025 15:30:12	Finished building JB-GPC-JOB1-354.