childers
commented
10 years ago I exported the annotations for this scaffold as gff3 to see what was happening at the feature level. There is a non_canonical_three_prime_splice_site feature located at coordinated that would put it inside a CDS/exon boundary.
It is possible that this happened due to the user adjusting the boundary, creating the non-canonical splice site flag. For some reason the non_canonical_three_prime_splice_site state was not properly reset when the feature was later adjusted.
nathandunn
monicacecilia
After inspecting a gene model on the bedbug instance of Web Apollo, I learned that Apollo is acting as though there is an intron of length = 0bp. (the previous exon "ends" one position (bp) before). I discovered the error by using the square brackets [] to move between exons.
Below are Console erros, as well as the fragment of the .css that describes non-canonical warning in the offending exon.
This is what the "non canonical" image looks like, located in the middle of an exon. Apollo seems to think that there is an intron of length = 0bp, and it is indicating that it has non-canonical splice sites.
The element in the css style sheet is identified as:
Elements element.style { left: 3.333818605328286%; width: 0%; } .noncanonical-splice-site, .plus-noncanonical-splice-site, .minus-noncanonical-splice-site { margin-left: -8px; /* margin-top: -11px; _/ margin-top: 9px; padding-left: 8px; padding-right: 8px; position: absolute; height: 16px; z-index: 100; background-color: transparent; background-image: url('../img/exclamation_circleorange.png'); pointer-events: none; / background-image: url('img/exclamation_circleorange.png'); / /_ background-image: url('img/warning_exclamationsmall.png'); / /_ background-image: url('img/warningexclamation.png'); / /_ background-image: url('img/marker_roundedred.png'); / /_ background-image: url('img/marker_squared_red.png'); */ } .subfeature, .plus-subfeature, .minus-subfeature { position: absolute; background-color: #dadada; height: 7px; min-width: 1px; z-index: 12; box-sizing: border-box; -moz-box-sizing: border-box; -webkit-box-sizing: border-box; -ms-box-sizing: border-box; } body, div, dl, dt, dd, li, h1, h2, h3, h4, h5, h6, pre, form, fieldset, input, textarea, p, blockquote, th, td { margin: 0; padding: 0; } user agent stylesheetdiv { display: block; } Inherited from div.feature.plus-annot.ui-droppable .feature, .plus-feature, .minus-feature { position: absolute; height: 7px; background-repeat: repeat-x; cursor: pointer; min-width: 1px; z-index: 10; background-color: #eee; box-sizing: border-box; -moz-box-sizing: border-box; -webkit-box-sizing: border-box; -ms-box-sizing: border-box; } Inherited from div.trackContainer.innerTrackContainer.draggable.dojoDndSource.dojoDndTarget.dojoDndContainerOver .draggable { cursor: move; } Inherited from body.tundra html, body { height: 100%; width: 100%; padding: 0; border: 0; font-size: 12px; font-family: Univers,Trebuchet MS,Helvetica,Arial,sans-serif; } body { font: 12px Myriad,Helvetica,Tahoma,Arial,clean,sans-serif; } Inherited from html.dj_webkit.dj_chrome.dj_contentbox.has-webkit.has-no-quirks html, body { height: 100%; width: 100%; padding: 0; border: 0; font-size: 12px; font-family: Univers,Trebuchet MS,Helvetica,Arial,sans-serif; }
The error console looks like this:
Error Console: loaded WebApollo plugin main.js:36 In JBrowse configuration, datasets specified, but dataset_id not set. Dataset selector will not be shown. Browser.js:550 The page at 'https://apollo.nal.usda.gov/cimlec/jbrowse/?loc=Scaffold4%3A8930608..894284…%2CTranscriptome%20models%2Ccimlec_RNA_female%2Ccimlec_RNA_male&highlight=' was loaded over HTTPS, but displayed insecure content from 'http://jbrowse.org/analytics/clientReport?ver=development&refSeqs-count=140…FWiggle%2FDensity=2&track-types-JBrowse%2FView%2FTrack%2FWiggle%2FXYPlot=1': this content should also be loaded over HTTPS. ?loc=Scaffold4%3A8930608..8942847&tracks=DNA%2CAnnotations%2Ccimlec_current_models%2Caugustus_maske…:1 Store statistics: Clec_RNA-Adult-Female_300Bp_ICD_CLI5RP.bam Object GlobalStatsEstimationMixin.js:55 Store statistics: Clec_RNA-Adult-Male_300Bp_ICD_CLI5RP.bam Object {featureDensity: 0.0253515625, _statsSampleFeatures: 649, _statsSampleInterval: Object} GlobalStatsEstimationMixin.js:55 GET https://apollo.nal.usda.gov/cimlec/jbrowse/data/seq/140/168/b9/Scaffold4-446.txt net::ERR_CONNECTION_TIMED_OUT xhr.js:206 xhr xhr.js:206 provider.(anonymous function) util.js:101 declare._fetchChunk SequenceChunks.js:113 (anonymous function) SequenceChunks.js:86 declare.getFeatures SequenceChunks.js:105 declare.getReferenceSequence SeqFeature.js:169 declare.fillBlock SequenceTrack.js:380 declare._showBlock BlockBased.js:554 declare.showRange BlockBased.js:281 inherited declare.js:189 declare.showRange DraggableHTMLFeatures.js:1092 (anonymous function) GenomeView.js:2000 declare.trackIterate GenomeView.js:2249 declare.showVisibleBlocks GenomeView.js:1999 declare.zoomUpdate GenomeView.js:1913 (anonymous function) GenomeView.js:1792 Animation.stop Animation.js:62 Animation.animate Animation.js:30 Animation.animFunction
After attempting to modify the boundary to go from 5' end towards the 3' end of the offending exon, and trying to pass the 'non-canonical' features, the error log included a "SyntaxError" due to an "Unexpected token", which I imagine was caused by the non-canonical signal.
This is the error log in the console:
SyntaxError {stack: (...), message: "Unexpected token <"} message: "Unexpected token <" stack: (...) get stack: function () { [native code] } set stack: function () { [native code] } proto: Error "SyntaxError: Unexpected token < at declare.handleError (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4428:54) at https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:5534:16 at signalListener (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/Deferred.js:37:21) at signalWaiting (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/Deferred.js:28:4) at reject.reject (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/Deferred.js:219:5) at signalDeferred (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/Deferred.js:84:15) at signalListener (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/Deferred.js:58:4) at signalWaiting (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/Deferred.js:28:4) at reject.reject (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/Deferred.js:219:5) at signalDeferred (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/Deferred.js:84:15)
Error at Promise.then.promise.then (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/Deferred.js:252:24) at declare.executeUpdateOperation (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:5526:12) at HTMLDivElement.$.resizable.stop (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:767:31) at Object.$.Widget._trigger (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/jslib/jqueryui/widget.js:268:13) at Object.$.widget._propagate (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/jslib/jqueryui/resizable.js:525:26) at Object.$.widget._mouseStop (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/jslib/jqueryui/resizable.js:342:8) at Object.$.widget._mouseUp (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/jslib/jqueryui/mouse.js:138:9) at HTMLDocument._mouseUpDelegate (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/jslib/jqueryui/mouse.js:94:16) at HTMLDocument.jQuery.event.dispatch (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/jslib/jquery/jquery.js:3256:9) at HTMLDocument.elemData.handle.eventHandle (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/jslib/jquery/jquery.js:2875:46)" instrumentation.js:18
I then tried to pull up the Annotation Information Editor,
First, the request was not sent to the server. Later, Web Apollo failed at retrieving the AIE, and threw two errors. These three errors are shown below:
POST https://apollo.nal.usda.gov/cimlec/AnnotationEditorService xhr.js:206 xhr xhr.js:206 dojo.xhr xhr.js:607 dojo.rawXhrPost.dojo.xhrPost xhr.js:644 declare.getAnnotationInfoEditorConfigs AnnotTrack.js:2024 declare.getAnnotationInfoEditorForSelectedFeatures AnnotTrack.js:1997 declare.getAnnotationInfoEditor AnnotTrack.js:1985 annot_context_menu.addChild.dijit.MenuItem.onClick AnnotTrack.js:4730 declare.onItemClick _MenuBase.js:258 (anonymous function) _MenuBase.js:65 (anonymous function) on.js:198 (anonymous function) a11yclick.js:84 DOMException {message: "Failed to execute 'send' on 'XMLHttpRequest': Fail…llo.nal.usda.gov/cimlec/AnnotationEditorService'.", name: "NetworkError", code: 19, stack: "Error: Failed to execute 'send' on 'XMLHttpRequest….gov/cimlec/jbrowse/src/dijit/_MenuBase.js:65:10)", response: Object…} code: 19 message: "Failed to execute 'send' on 'XMLHttpRequest': Failed to load 'https://apollo.nal.usda.gov/cimlec/AnnotationEditorService'." name: "NetworkError" response: Object responseText: undefined stack: "Error: Failed to execute 'send' on 'XMLHttpRequest': Failed to load 'https://apollo.nal.usda.gov/cimlec/AnnotationEditorService'.↵ at Error (native)↵ at xhr (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/request/xhr.js:206:9)↵ at Object.dojo.xhr (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/_base/xhr.js:607:11)↵ at Object.dojo.rawXhrPost.dojo.xhrPost (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dojo/_base/xhr.js:644:15)↵ at declare.getAnnotationInfoEditorConfigs (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:2024:11)↵ at declare.getAnnotationInfoEditorForSelectedFeatures (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:1997:15)↵ at declare.getAnnotationInfoEditor (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:1985:14)↵ at annot_context_menu.addChild.dijit.MenuItem.onClick (https://apollo.nal.usda.gov/cimlec/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4730:16)↵ at declare.onItemClick (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dijit/_MenuBase.js:258:46)↵ at HTMLTableRowElement. (https://apollo.nal.usda.gov/cimlec/jbrowse/src/dijit/_MenuBase.js:65:10)"
status: undefined
xhr: XMLHttpRequest
proto: DOMException
xhr.js:432
_deferError xhr.js:432
(anonymous function) xhr.js:392
notify Deferred.js:187
complete Deferred.js:168
reject.errback Deferred.js:230
notify Deferred.js:202
complete Deferred.js:168
reject.errback Deferred.js:230
notify Deferred.js:202
complete Deferred.js:168
reject.errback Deferred.js:230
(anonymous function) xhr.js:627
signalListener Deferred.js:37
then.promise.then Deferred.js:258
lang.extend.otherwise Promise.js:115
dojo.xhr xhr.js:620
dojo.rawXhrPost.dojo.xhrPost xhr.js:644
declare.getAnnotationInfoEditorConfigs AnnotTrack.js:2024
declare.getAnnotationInfoEditorForSelectedFeatures AnnotTrack.js:1997
declare.getAnnotationInfoEditor AnnotTrack.js:1985
annot_context_menu.addChild.dijit.MenuItem.onClick AnnotTrack.js:4730
declare.onItemClick _MenuBase.js:258
(anonymous function) _MenuBase.js:65
(anonymous function) on.js:198
(anonymous function) a11yclick.js:84
TypeError {stack: (...), message: "Cannot read property 'sequence:gene' of undefined"}
xhr.js:432
_deferError xhr.js:432
(anonymous function) xhr.js:392
notify Deferred.js:187
complete Deferred.js:168
reject.errback Deferred.js:230
notify Deferred.js:198
complete Deferred.js:168
resolve.callback Deferred.js:215
notify Deferred.js:196
complete Deferred.js:168
resolve.callback Deferred.js:215
(anonymous function) xhr.js:619
signalListener Deferred.js:37
then.promise.then Deferred.js:258
dojo.xhr xhr.js:618
dojo.rawXhrPost.dojo.xhrPost xhr.js:644
init AnnotTrack.js:2137
declare.createAnnotationInfoEditorPanelForFeature AnnotTrack.js:3833
declare.getAnnotationInfoEditorForSelectedFeatures AnnotTrack.js:2002
declare.getAnnotationInfoEditor AnnotTrack.js:1985
annot_context_menu.addChild.dijit.MenuItem.onClick AnnotTrack.js:4730
declare.onItemClick _MenuBase.js:258
(anonymous function) _MenuBase.js:65
(anonymous function) on.js:198
(anonymous function) a11yclick.js:84
TypeError {stack: (...), message: "Cannot read property 'sequence:mRNA' of undefined"}
message: "Cannot read property 'sequence:mRNA' of undefined"
stack: (...)
get stack: function () { [native code] }
set stack: function () { [native code] }
proto: Error
xhr.js:432
_deferError xhr.js:432
(anonymous function) xhr.js:392
notify Deferred.js:187
complete Deferred.js:168
reject.errback Deferred.js:230
notify Deferred.js:198
complete Deferred.js:168
resolve.callback Deferred.js:215
notify Deferred.js:196
complete Deferred.js:168
resolve.callback Deferred.js:215
(anonymous function) xhr.js:619
signalListener Deferred.js:37
then.promise.then Deferred.js:258
dojo.xhr xhr.js:618
dojo.rawXhrPost.dojo.xhrPost xhr.js:644
init AnnotTrack.js:2137
declare.createAnnotationInfoEditorPanelForFeature AnnotTrack.js:3833
declare.getAnnotationInfoEditorForSelectedFeatures AnnotTrack.js:2007
declare.getAnnotationInfoEditor AnnotTrack.js:1985
annot_context_menu.addChild.dijit.MenuItem.onClick AnnotTrack.js:4730
declare.onItemClick _MenuBase.js:258
(anonymous function) _MenuBase.js:65
(anonymous function) on.js:198
(anonymous function) a11yclick.js:84
Later, Web Apollo did not let me grab an exon to add it to a feature. I was unable to drag the element from the Evidence tracks (any evidence tracks) to add it as an exon to the desired new annotation.
The error went away after reloading and cleaning the cache.
the errors in the console read like so (repeatedly):
Uncaught TypeError: Cannot read property 'domNode' of null DraggableHTMLFeatures.js:917 declare.handleFeatureDragSetup DraggableHTMLFeatures.js:917 declare.onFeatureMouseDown DraggableHTMLFeatures.js:787 (anonymous function) lang.js:373 jQuery.event.dispatch jquery.js:3256 elemData.handle.eventHandle jquery.js:2876
It is not possible to retrieve the entire Sequence of the gene model with the fake intron. An "Unexpected token" is also apparent and disruptive.
The error console reads:
SyntaxError {stack: (...), message: "Unexpected token <"} message: "Unexpected token <" stack: (...) get stack: function () { [native code] } arguments: null caller: null length: 0 name: "" prototype: Object constructor: function () { [native code] } arguments: null caller: null length: 0 name: "" prototype: Object constructor: function () { [native code] } arguments: null caller: null length: 0 name: "" prototype: Object proto: function Empty() {}