Increasing max memory inside container?

[marchoeppner]

Hi,
I have been running the WA docker container successfully for some time. Now I wanted to implement a backup routine for the curation track of a vertebrate genome (> 20.000 models). I get a an out of memory error when doing this from outside the container using the groovy get_gff3.groovy script that is bundled with WA.

The machine has plenty RAM, but I think the tomcat server inside the docker container is configured with too little.

Since I have little experience with Docker - can I somwhow increase the max memory available to Tomcat inside the container?

Cheers,
Marc

[nathandunn]

I haven’t done it, but if you are able to figure out a solution, please open a PR for it, as I think at least GB would be useful. https://stackoverflow.com/questions/29923531/how-to-set-java-heap-size-xms-xmx-inside-docker-container <https://stackoverflow.com/questions/29923531/how-to-set-java-heap-size-xms-xmx-inside-docker-container> Nathan

…

On Nov 27, 2018, at 3:45 AM, marchoeppner ***@***.***> wrote: Hi, I have been running the WA docker container successfully for some time. Now I wanted to implement a backup routine for the curation track of a vertebrate genome (> 20.000 models). I get a an out of memory error when doing this from outside the container using the groovy get_gff3.groovy script that is bundled with WA. The machine has plenty RAM, but I think the tomcat server inside the docker container is configured with too little. Since I have little experience with Docker - I can I increase the max memory available to Tomcat inside the container? Cheers, Marc — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#31>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAt2qsKTuAQviX1MjSoEWiaWKDZnvcQ1ks5uzSXzgaJpZM4Y1UaM>.

[nathandunn]

@marchoeppner Most likely you'll be updating the launch.sh script. I'm sure there will be several ways to do it. Unfortunately, I have to look at other stuff.

Might be worth posting to the Apollo list, though, as someone there has already done this.

[hodgett]

Has anyone figured this one out yet? I have tried passing JAVA_OPTS and CATALINA_OPTS using -e but they don't take. The memory allocated is way too small to handle the datasets and I get the following err for the bam track;

[nathandunn]

@hodgett are you sure its memory related? Can you show me the catalina.out and the javascript console?

[hodgett]

Where do I find these?

[hodgett]

`Loaded Chado
Restarting tomcat with /var/lib/tomcat8
[FAIL] Starting Tomcat servlet engine: tomcat8 failed!
01-Mar-2019 21:09:27.539 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/share/tomcat8
01-Mar-2019 21:09:27.539 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/tmp/tomcat8-tomcat8-tmp
01-Mar-2019 21:09:27.539 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
01-Mar-2019 21:09:27.625 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
01-Mar-2019 21:09:27.652 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
01-Mar-2019 21:09:27.654 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 510 ms
01-Mar-2019 21:09:27.689 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service Catalina
01-Mar-2019 21:09:27.689 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.14 (Debian)
01-Mar-2019 21:09:27.706 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
01-Mar-2019 21:09:27.726 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 71 ms
01-Mar-2019 21:09:37.732 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive /var/lib/tomcat8/webapps/apollo.war
01-Mar-2019 21:09:47.507 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Configuring Shiro ...

Shiro Configured
2019-03-01 21:10:17,198 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add column cvterm_id int8 not null
2019-03-01 21:10:17,200 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" contains null values
2019-03-01 21:10:17,211 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm
2019-03-01 21:10:17,211 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist
Starting Quartz Scheduler in QuartzFactoryBean
2019-03-01 21:10:28,170 [localhost-startStop-1] WARN apollo.UserService - User exists admin@local.host and can not be added again.
2019-03-01 21:10:29,237 [localhost-startStop-1] WARN apollo.PhoneHomeService - Failed to phone home: org.springframework.transaction.HeuristicCompletionException: Heuristic completion: outcome state is mixed; nested exception is org.springframework.orm.hibernate4.HibernateOptimisticLockingFailureException: Object of class [org.bbop.apollo.ServerData] with identifier [150]: optimistic locking failed; nested exception is org.hibernate.StaleObjectStateException: Row was updated or deleted by another transaction (or unsaved-value mapping was incorrect) : [org.bbop.apollo.ServerData#150]
2019-03-01 21:10:29,269 [Actor Thread 3] ERROR apollo.PhoneHomeService - An error occured while phoning home Heuristic completion: outcome state is mixed; nested exception is org.springframework.orm.hibernate4.HibernateOptimisticLockingFailureException: Object of class [org.bbop.apollo.ServerData] with identifier [150]: optimistic locking failed; nested exception is org.hibernate.StaleObjectStateException: Row was updated or deleted by another transaction (or unsaved-value mapping was incorrect) : [org.bbop.apollo.ServerData#150]
01-Mar-2019 21:10:29.429 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /var/lib/tomcat8/webapps/apollo.war has finished in 51,696 ms
2019-03-01 21:10:44,864 [http-nio-8080-exec-3] WARN apollo.PreferenceService - No user present, so using the client token
2019-03-01 21:10:44,941 [http-nio-8080-exec-4] ERROR apollo.PermissionService - Username not supplied so can not authenticate.
2019-03-01 21:10:44,964 [http-nio-8080-exec-9] WARN apollo.PermissionService - Failed to authenticate user
2019-03-01 21:10:45,055 [http-nio-8080-exec-6] ERROR apollo.PermissionService - Username not supplied so can not authenticate.
2019-03-01 21:11:05,786 [http-nio-8080-exec-6] WARN apollo.PermissionService - Failed to authenticate user
2019-03-01 21:11:05,787 [http-nio-8080-exec-6] WARN apollo.SecurityFilters - Authentication failed
2019-03-01 21:11:16,696 [http-nio-8080-exec-10] INFO apollo.UserController - updateTrackListPreference
2019-03-01 21:11:16,703 [http-nio-8080-exec-10] INFO apollo.UserController - Added userOrganismPreference false
2019-03-01 21:11:24,786 [http-nio-8080-exec-7] ERROR apollo.JbrowseController - File not found: /data/NbAnnotFeb2019/tracks/Gmp_NbV1-genes/NbV1Ch13/trackData.json
01-Mar-2019 21:14:25.436 INFO [MessageBrokerSockJS-2] org.apache.coyote.AbstractProcessor.setErrorState An error occurred in processing while on a non-container thread. The connection will be closed immediately
java.io.IOException: Broken pipe
at sun.nio.ch.FileDispatcherImpl.write0(Native Method)
at sun.nio.ch.SocketDispatcher.write(SocketDispatcher.java:47)
at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:93)
at sun.nio.ch.IOUtil.write(IOUtil.java:65)
at sun.nio.ch.SocketChannelImpl.write(SocketChannelImpl.java:471)
at org.apache.tomcat.util.net.NioChannel.write(NioChannel.java:134)
at org.apache.tomcat.util.net.NioBlockingSelector.write(NioBlockingSelector.java:101)
at org.apache.tomcat.util.net.NioSelectorPool.write(NioSelectorPool.java:157)
at org.apache.tomcat.util.net.NioEndpoint$NioSocketWrapper.doWrite(NioEndpoint.java:1262)
at org.apache.tomcat.util.net.SocketWrapperBase.doWrite(SocketWrapperBase.java:670)
at org.apache.tomcat.util.net.SocketWrapperBase.flushBlocking(SocketWrapperBase.java:607)
at org.apache.tomcat.util.net.SocketWrapperBase.flush(SocketWrapperBase.java:597)
at org.apache.coyote.http11.Http11OutputBuffer.flushBuffer(Http11OutputBuffer.java:581)
at org.apache.coyote.http11.Http11OutputBuffer.flush(Http11OutputBuffer.java:272)
at org.apache.coyote.http11.Http11Processor.flush(Http11Processor.java:1506)
at org.apache.coyote.AbstractProcessor.action(AbstractProcessor.java:279)
at org.apache.coyote.Response.action(Response.java:172)
at org.apache.catalina.connector.OutputBuffer.doFlush(OutputBuffer.java:317)
at org.apache.catalina.connector.OutputBuffer.flush(OutputBuffer.java:284)
at org.apache.catalina.connector.Response.flushBuffer(Response.java:541)
at org.apache.catalina.connector.ResponseFacade.flushBuffer(ResponseFacade.java:312)
at org.springframework.http.server.ServletServerHttpResponse.flush(ServletServerHttpResponse.java:91)
at org.springframework.web.socket.sockjs.transport.session.AbstractHttpSockJsSession.writeFrameInternal(AbstractHttpSockJsSession.java:345)
at org.springframework.web.socket.sockjs.transport.session.AbstractSockJsSession.writeFrame(AbstractSockJsSession.java:325)
at org.springframework.web.socket.sockjs.transport.session.AbstractSockJsSession.sendHeartbeat(AbstractSockJsSession.java:249)
at org.springframework.web.socket.sockjs.transport.session.AbstractSockJsSession$1.run(AbstractSockJsSession.java:269)
at org.springframework.scheduling.support.DelegatingErrorHandlingRunnable.run(DelegatingErrorHandlingRunnable.java:54)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)`

[hodgett]

I don't know where to find catalina.out, the one on my host is zero length

[nathandunn]

@hodgett In this case, what you are are seeing above is the catalina.out.

1. What are you seeing in the javascript console of your browser?
2. What did your raw source data file look like?
3. How did you process the tracks?
4. If you turn off that track, does everything seem to work normally (a zoomed out screenshot would confirm this).

Thanks.

[hodgett]

From the system info I see;
Max memory | 6257.246208 MB
Free memory | 145.815840 MB
Available processors | 2
Total memory | 636.080128 MB

I would like to increase the total memory like I have seen in other apollo installs, 636Mb is way too small. The BAM file is 250Gb. Only this track is showing the error, the other tracks display fine in the same window.
{ "baiUrlTemplate" : "raw/NbRNASeq_AllS.sorted.bam.bai", "key" : "NbRNASeq_AllS.sorted", "label" : "NbRNASeq_AllS.sorted", "storeClass" : "JBrowse/Store/SeqFeature/BAM", "type" : "JBrowse/View/Track/Alignments2", "urlTemplate" : "raw/NbRNASeq_AllS.sorted.bam" }

[nathandunn]

That bam size won’t necessarily affect memory. You need the chrome JavaScript console to see what the error is.

…

On Mar 1, 2019, at 8:35 PM, hodgett ***@***.***> wrote: From the system info I see; Max memory | 6257.246208 MB Free memory | 145.815840 MB Available processors | 2 Total memory | 636.080128 MB I would like to increase the total memory like I have seen in other apollo installs, 636Mb is way too small. The BAM file is 250Gb. Only this track is showing the error, the other tracks display fine in the same window. { "baiUrlTemplate" : "raw/NbRNASeq_AllS.sorted.bam.bai", "key" : "NbRNASeq_AllS.sorted", "label" : "NbRNASeq_AllS.sorted", "storeClass" : "JBrowse/Store/SeqFeature/BAM", "type" : "JBrowse/View/Track/Alignments2", "urlTemplate" : "raw/NbRNASeq_AllS.sorted.bam" } — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[hodgett]

BlockBased.js:376 TypeError: Failed to fetch TypeError: Failed to fetch _handleError @ BlockBased.js:376 inherited @ declare.js:214 _handleError @ CanvasFeatures.js:231 errorCallback @ CanvasFeatures.js:460 Promise.catch (async) _getFeatures @ BAM.js:346 (anonymous) @ lang.js:337 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 getFeatures @ DeferredFeaturesMixin.js:31 fillFeatures @ CanvasFeatures.js:511 inherited @ declare.js:214 fillFeatures @ Alignments2.js:392 (anonymous) @ CanvasFeatures.js:208 (anonymous) @ lang.js:385 _getGlobalStats @ DeferredStatsMixin.js:36 (anonymous) @ lang.js:337 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 getGlobalStats @ DeferredStatsMixin.js:32 fillBlock @ CanvasFeatures.js:219 _showBlock @ BlockBased.js:484 (anonymous) @ BlockBased.js:244 showRange @ BlockBased.js:243 (anonymous) @ GenomeView.js:1820 (anonymous) @ GenomeView.js:1819 trackIterate @ GenomeView.js:2122 showVisibleBlocks @ GenomeView.js:1818 updateTrackList @ GenomeView.js:2219 showTracks @ GenomeView.js:1859 (anonymous) @ lang.js:383 dispatcher @ aspect.js:101 on.emit @ on.js:344 on.emit @ on.js:385 emit @ Evented.js:32 publish @ topic.js:25 publish @ Browser.js:1724 (anonymous) @ Browser.js:1465 dispatcher @ aspect.js:101 on.emit @ on.js:344 on.emit @ on.js:385 emit @ Evented.js:32 publish @ topic.js:25 publish @ Browser.js:1724 itemClick @ Hierarchical.js:186 (anonymous) @ Hierarchical.js:175 BlockBased.js:376 TypeError: Failed to fetch TypeError: Failed to fetch _handleError @ BlockBased.js:376 inherited @ declare.js:214 _handleError @ CanvasFeatures.js:231 errorCallback @ CanvasFeatures.js:460 Promise.catch (async) _getFeatures @ BAM.js:346 (anonymous) @ lang.js:337 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 getFeatures @ DeferredFeaturesMixin.js:31 fillFeatures @ CanvasFeatures.js:511 inherited @ declare.js:214 fillFeatures @ Alignments2.js:392 (anonymous) @ CanvasFeatures.js:208 (anonymous) @ lang.js:385 _getGlobalStats @ DeferredStatsMixin.js:36 (anonymous) @ lang.js:337 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 getGlobalStats @ DeferredStatsMixin.js:32 fillBlock @ CanvasFeatures.js:219 _showBlock @ BlockBased.js:484 (anonymous) @ BlockBased.js:244 showRange @ BlockBased.js:243 (anonymous) @ GenomeView.js:1820 (anonymous) @ GenomeView.js:1819 trackIterate @ GenomeView.js:2122 showVisibleBlocks @ GenomeView.js:1818 updateTrackList @ GenomeView.js:2219 showTracks @ GenomeView.js:1859 (anonymous) @ lang.js:383 dispatcher @ aspect.js:101 on.emit @ on.js:344 on.emit @ on.js:385 emit @ Evented.js:32 publish @ topic.js:25 publish @ Browser.js:1724 (anonymous) @ Browser.js:1465 dispatcher @ aspect.js:101 on.emit @ on.js:344 on.emit @ on.js:385 emit @ Evented.js:32 publish @ topic.js:25 publish @ Browser.js:1724 itemClick @ Hierarchical.js:186 (anonymous) @ Hierarchical.js:175 BlockBased.js:376 TypeError: Failed to fetch TypeError: Failed to fetch _handleError @ BlockBased.js:376 inherited @ declare.js:214 _handleError @ CanvasFeatures.js:231 errorCallback @ CanvasFeatures.js:460 Promise.catch (async) _getFeatures @ BAM.js:346 (anonymous) @ lang.js:337 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 getFeatures @ DeferredFeaturesMixin.js:31 fillFeatures @ CanvasFeatures.js:511 inherited @ declare.js:214 fillFeatures @ Alignments2.js:392 (anonymous) @ CanvasFeatures.js:208 (anonymous) @ lang.js:385 _getGlobalStats @ DeferredStatsMixin.js:36 (anonymous) @ lang.js:337 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 getGlobalStats @ DeferredStatsMixin.js:32 fillBlock @ CanvasFeatures.js:219 _showBlock @ BlockBased.js:484 (anonymous) @ BlockBased.js:244 showRange @ BlockBased.js:243 (anonymous) @ GenomeView.js:1820 (anonymous) @ GenomeView.js:1819 trackIterate @ GenomeView.js:2122 showVisibleBlocks @ GenomeView.js:1818 updateTrackList @ GenomeView.js:2219 showTracks @ GenomeView.js:1859 (anonymous) @ lang.js:383 dispatcher @ aspect.js:101 on.emit @ on.js:344 on.emit @ on.js:385 emit @ Evented.js:32 publish @ topic.js:25 publish @ Browser.js:1724 (anonymous) @ Browser.js:1465 dispatcher @ aspect.js:101 on.emit @ on.js:344 on.emit @ on.js:385 emit @ Evented.js:32 publish @ topic.js:25 publish @ Browser.js:1724 itemClick @ Hierarchical.js:186 (anonymous) @ Hierarchical.js:175 BlockBased.js:376 TypeError: Failed to fetch TypeError: Failed to fetch _handleError @ BlockBased.js:376 inherited @ declare.js:214 _handleError @ CanvasFeatures.js:231 errorCallback @ CanvasFeatures.js:460 Promise.catch (async) _getFeatures @ BAM.js:346 (anonymous) @ lang.js:337 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 getFeatures @ DeferredFeaturesMixin.js:31 fillFeatures @ CanvasFeatures.js:511 inherited @ declare.js:214 fillFeatures @ Alignments2.js:392 (anonymous) @ CanvasFeatures.js:208 (anonymous) @ lang.js:385 _getGlobalStats @ DeferredStatsMixin.js:36 (anonymous) @ lang.js:337 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 getGlobalStats @ DeferredStatsMixin.js:32 fillBlock @ CanvasFeatures.js:219 _showBlock @ BlockBased.js:484 (anonymous) @ BlockBased.js:244 showRange @ BlockBased.js:243 (anonymous) @ GenomeView.js:1820 (anonymous) @ GenomeView.js:1819 trackIterate @ GenomeView.js:2122 showVisibleBlocks @ GenomeView.js:1818 updateTrackList @ GenomeView.js:2219 showTracks @ GenomeView.js:1859 (anonymous) @ lang.js:383 dispatcher @ aspect.js:101 on.emit @ on.js:344 on.emit @ on.js:385 emit @ Evented.js:32 publish @ topic.js:25 publish @ Browser.js:1724 (anonymous) @ Browser.js:1465 dispatcher @ aspect.js:101 on.emit @ on.js:344 on.emit @ on.js:385 emit @ Evented.js:32 publish @ topic.js:25 publish @ Browser.js:1724 itemClick @ Hierarchical.js:186 (anonymous) @ Hierarchical.js:175

[hodgett]

tenacious-fetch.m.js:2 GET https://sefapps06.qut.edu.au/apollo/31/jbrowse/data/raw/NbRNASeq_AllS.sorted.bam.bai net::ERR_CONTENT_LENGTH_MISMATCH 200 t @ tenacious-fetch.m.js:2 (anonymous) @ tenacious-fetch.m.js:2 t @ tenacious-fetch.m.js:2 (anonymous) @ tenacious-fetch.m.js:2 getfetch @ XHRBlob.js:30 _callee$ @ XHRBlob.js:209 tryCatch @ runtime.js:65 invoke @ runtime.js:303 prototype.(anonymous function) @ runtime.js:117 step @ XHRBlob.js:3 (anonymous) @ XHRBlob.js:3 (anonymous) @ XHRBlob.js:3 fetchBufferPromise @ XHRBlob.js:235 _callee2$ @ BlobFilehandleWrapper.js:65 tryCatch @ runtime.js:65 invoke @ runtime.js:303 prototype.(anonymous function) @ runtime.js:117 step @ BlobFilehandleWrapper.js:3 (anonymous) @ BlobFilehandleWrapper.js:3 (anonymous) @ BlobFilehandleWrapper.js:3 readFile @ BlobFilehandleWrapper.js:76 _callee2$ @ bai.js:121 tryCatch @ runtime.js:62 invoke @ runtime.js:296 prototype.(anonymous function) @ runtime.js:114 step @ asyncToGenerator.js:17 (anonymous) @ asyncToGenerator.js:35 F @ _export.js:36 (anonymous) @ asyncToGenerator.js:14 parse @ bai.js:201 _tinyMemoized @ bai.js:408 _callee4$ @ bai.js:343 tryCatch @ runtime.js:62 invoke @ runtime.js:296 prototype.(anonymous function) @ runtime.js:114 step @ asyncToGenerator.js:17 (anonymous) @ asyncToGenerator.js:35 F @ _export.js:36 (anonymous) @ asyncToGenerator.js:14 hasRefSeq @ bai.js:368 hasRefSeq @ bamFile.js:650 constructor @ BAM.js:233 (anonymous) @ declare.js:426 (anonymous) @ Browser.js:1622 (anonymous) @ lang.js:385 contextRequire @ main.bundle.js:313 req @ main.bundle.js:212 getStore @ Browser.js:1613 renderTrack @ GenomeView.js:2069 (anonymous) @ GenomeView.js:177 (anonymous) @ lang.js:385 _normalizedCreator @ Container.js:343 _normalizedCreator @ Selector.js:155 insertNodes @ Container.js:192 insertNodes @ Selector.js:172 showTracks @ GenomeView.js:1857 (anonymous) @ lang.js:383 dispatcher @ aspect.js:101 on.emit @ on.js:344 on.emit @ on.js:385 emit @ Evented.js:32 publish @ topic.js:25 publish @ Browser.js:1724 (anonymous) @ Browser.js:2380 (anonymous) @ lang.js:385 (anonymous) @ Browser.js:1818 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:902 (anonymous) @ lang.js:385 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 (anonymous) @ Browser.js:890 (anonymous) @ lang.js:385 (anonymous) @ Browser.js:1818 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 afterMilestone @ Browser.js:1816 (anonymous) @ Browser.js:889 (anonymous) @ lang.js:385 (anonymous) @ Browser.js:1818 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:498 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 handleResponse @ xhr.js:81 onLoad @ xhr.js:116 load (async) addListeners @ xhr.js:144 xhr @ xhr.js:231 (anonymous) @ Browser.js:491 _milestoneFunction @ Browser.js:1792 loadRefSeqs @ Browser.js:448 (anonymous) @ Browser.js:88 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 (anonymous) @ Browser.js:85 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:246 notify @ Deferred.js:187 complete @ Deferred.js:168 resolve.callback @ Deferred.js:248 addResult @ DeferredList.js:54 (anonymous) @ DeferredList.js:37 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:277 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:542 finish @ lazyload.js:114 pollWebKit @ lazyload.js:329 setTimeout (async) pollWebKit @ lazyload.js:338 setTimeout (async) pollWebKit @ lazyload.js:338 load @ lazyload.js:250 finish @ lazyload.js:116 pollWebKit @ lazyload.js:329 setTimeout (async) pollWebKit @ lazyload.js:338 load @ lazyload.js:250 css @ lazyload.js:367 _loadCSS @ Browser.js:541 (anonymous) @ Browser.js:269 forEach @ array.js:247 (anonymous) @ Browser.js:252 (anonymous) @ lang.js:385 contextRequire @ main.bundle.js:313 req @ main.bundle.js:212 (anonymous) @ Browser.js:249 _milestoneFunction @ Browser.js:1792 initPlugins @ Browser.js:191 (anonymous) @ Browser.js:83 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:1882 (anonymous) @ lang.js:385 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ all.js:69 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ all.js:69 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ all.js:69 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 signalListener @ Deferred.js:45 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 handleResponse @ xhr.js:81 onLoad @ xhr.js:116 load (async) addListeners @ xhr.js:144 xhr @ xhr.js:231 load @ JB_json_v1.js:28 (anonymous) @ ConfigManager.js:144 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 _loadInclude @ ConfigManager.js:141 (anonymous) @ ConfigManager.js:123 _loadRecur @ ConfigManager.js:121 (anonymous) @ ConfigManager.js:124 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 handleResponse @ xhr.js:81 onLoad @ xhr.js:116 load (async) addListeners @ xhr.js:144 xhr @ xhr.js:231 load @ JB_json_v1.js:28 (anonymous) @ ConfigManager.js:144 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 _loadInclude @ ConfigManager.js:141 (anonymous) @ ConfigManager.js:123 _loadRecur @ ConfigManager.js:121 (anonymous) @ ConfigManager.js:124 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 handleResponse @ xhr.js:81 onLoad @ xhr.js:116 load (async) addListeners @ xhr.js:144 xhr @ xhr.js:231 load @ JB_json_v1.js:28 (anonymous) @ ConfigManager.js:144 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 _loadInclude @ ConfigManager.js:141 (anonymous) @ ConfigManager.js:123 _loadRecur @ ConfigManager.js:121 _loadIncludes @ ConfigManager.js:135 (anonymous) @ ConfigManager.js:48 getFinalConfig @ ConfigManager.js:62 (anonymous) @ Browser.js:1860 _milestoneFunction @ Browser.js:1792 loadConfig @ Browser.js:1846 (anonymous) @ Browser.js:73 callback @ ready.js:121 onEvent @ ready.js:47 processQ @ domReady.js:49 detectReady @ domReady.js:62

[nathandunn]

Looks like an error reading the index. 1. Does this happen for smaller BAM tracks? 2. Does this happen for EVERY scaffold? 3. Does this happen for standalone JBrowse? I would download and install the latest version of JBrowse: http://jbrowse.org/ <http://jbrowse.org/> And point it at that directory and see if you see the same error. (You should be able to do an ./setup.sh && npm start) If the answer to #3 is yes, I would post the issue (and the command you used to generate it) to the mailing list or as a JBrowse issue (once you confirm it): http://jbrowse.org/contact.html <http://jbrowse.org/contact.html>

…

On Mar 2, 2019, at 5:07 AM, hodgett ***@***.***> wrote: tenacious-fetch.m.js:2 GET https://sefapps06.qut.edu.au/apollo/31/jbrowse/data/raw/NbRNASeq_AllS.sorted.bam.bai net::ERR_CONTENT_LENGTH_MISMATCH 200 t @ tenacious-fetch.m.js:2 (anonymous) @ tenacious-fetch.m.js:2 t @ tenacious-fetch.m.js:2 (anonymous) @ tenacious-fetch.m.js:2 getfetch @ XHRBlob.js:30 _callee$ @ XHRBlob.js:209 tryCatch @ runtime.js:65 invoke @ runtime.js:303 prototype.(anonymous function) @ runtime.js:117 step @ XHRBlob.js:3 (anonymous) @ XHRBlob.js:3 (anonymous) @ XHRBlob.js:3 fetchBufferPromise @ XHRBlob.js:235 _callee2$ @ BlobFilehandleWrapper.js:65 tryCatch @ runtime.js:65 invoke @ runtime.js:303 prototype.(anonymous function) @ runtime.js:117 step @ BlobFilehandleWrapper.js:3 (anonymous) @ BlobFilehandleWrapper.js:3 (anonymous) @ BlobFilehandleWrapper.js:3 readFile @ BlobFilehandleWrapper.js:76 _callee2$ @ bai.js:121 tryCatch @ runtime.js:62 invoke @ runtime.js:296 prototype.(anonymous function) @ runtime.js:114 step @ asyncToGenerator.js:17 (anonymous) @ asyncToGenerator.js:35 F @ _export.js:36 (anonymous) @ asyncToGenerator.js:14 parse @ bai.js:201 _tinyMemoized @ bai.js:408 _callee4$ @ bai.js:343 tryCatch @ runtime.js:62 invoke @ runtime.js:296 prototype.(anonymous function) @ runtime.js:114 step @ asyncToGenerator.js:17 (anonymous) @ asyncToGenerator.js:35 F @ _export.js:36 (anonymous) @ asyncToGenerator.js:14 hasRefSeq @ bai.js:368 hasRefSeq @ bamFile.js:650 constructor @ BAM.js:233 (anonymous) @ declare.js:426 (anonymous) @ Browser.js:1622 (anonymous) @ lang.js:385 contextRequire @ main.bundle.js:313 req @ main.bundle.js:212 getStore @ Browser.js:1613 renderTrack @ GenomeView.js:2069 (anonymous) @ GenomeView.js:177 (anonymous) @ lang.js:385 _normalizedCreator @ Container.js:343 _normalizedCreator @ Selector.js:155 insertNodes @ Container.js:192 insertNodes @ Selector.js:172 showTracks @ GenomeView.js:1857 (anonymous) @ lang.js:383 dispatcher @ aspect.js:101 on.emit @ on.js:344 on.emit @ on.js:385 emit @ Evented.js:32 publish @ topic.js:25 publish @ Browser.js:1724 (anonymous) @ Browser.js:2380 (anonymous) @ lang.js:385 (anonymous) @ Browser.js:1818 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:902 (anonymous) @ lang.js:385 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 (anonymous) @ Browser.js:890 (anonymous) @ lang.js:385 (anonymous) @ Browser.js:1818 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 afterMilestone @ Browser.js:1816 (anonymous) @ Browser.js:889 (anonymous) @ lang.js:385 (anonymous) @ Browser.js:1818 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:498 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 handleResponse @ xhr.js:81 onLoad @ xhr.js:116 load (async) addListeners @ xhr.js:144 xhr @ xhr.js:231 (anonymous) @ Browser.js:491 _milestoneFunction @ Browser.js:1792 loadRefSeqs @ Browser.js:448 (anonymous) @ Browser.js:88 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 (anonymous) @ Browser.js:85 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:246 notify @ Deferred.js:187 complete @ Deferred.js:168 resolve.callback @ Deferred.js:248 addResult @ DeferredList.js:54 (anonymous) @ DeferredList.js:37 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:277 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:542 finish @ lazyload.js:114 pollWebKit @ lazyload.js:329 setTimeout (async) pollWebKit @ lazyload.js:338 setTimeout (async) pollWebKit @ lazyload.js:338 load @ lazyload.js:250 finish @ lazyload.js:116 pollWebKit @ lazyload.js:329 setTimeout (async) pollWebKit @ lazyload.js:338 load @ lazyload.js:250 css @ lazyload.js:367 _loadCSS @ Browser.js:541 (anonymous) @ Browser.js:269 forEach @ array.js:247 (anonymous) @ Browser.js:252 (anonymous) @ lang.js:385 contextRequire @ main.bundle.js:313 req @ main.bundle.js:212 (anonymous) @ Browser.js:249 _milestoneFunction @ Browser.js:1792 initPlugins @ Browser.js:191 (anonymous) @ Browser.js:83 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ Browser.js:1882 (anonymous) @ lang.js:385 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ all.js:69 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ all.js:69 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 (anonymous) @ all.js:69 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 signalListener @ Deferred.js:45 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 handleResponse @ xhr.js:81 onLoad @ xhr.js:116 load (async) addListeners @ xhr.js:144 xhr @ xhr.js:231 load @ JB_json_v1.js:28 (anonymous) @ ConfigManager.js:144 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 _loadInclude @ ConfigManager.js:141 (anonymous) @ ConfigManager.js:123 _loadRecur @ ConfigManager.js:121 (anonymous) @ ConfigManager.js:124 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 handleResponse @ xhr.js:81 onLoad @ xhr.js:116 load (async) addListeners @ xhr.js:144 xhr @ xhr.js:231 load @ JB_json_v1.js:28 (anonymous) @ ConfigManager.js:144 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 _loadInclude @ ConfigManager.js:141 (anonymous) @ ConfigManager.js:123 _loadRecur @ ConfigManager.js:121 (anonymous) @ ConfigManager.js:124 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 (anonymous) @ Deferred.js:70 signalListener @ Deferred.js:37 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:58 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 signalDeferred @ Deferred.js:81 signalListener @ Deferred.js:52 signalWaiting @ Deferred.js:28 Deferred.resolve @ Deferred.js:192 handleResponse @ xhr.js:81 onLoad @ xhr.js:116 load (async) addListeners @ xhr.js:144 xhr @ xhr.js:231 load @ JB_json_v1.js:28 (anonymous) @ ConfigManager.js:144 signalListener @ Deferred.js:37 Deferred.then.promise.then @ Deferred.js:258 _loadInclude @ ConfigManager.js:141 (anonymous) @ ConfigManager.js:123 _loadRecur @ ConfigManager.js:121 _loadIncludes @ ConfigManager.js:135 (anonymous) @ ConfigManager.js:48 getFinalConfig @ ConfigManager.js:62 (anonymous) @ Browser.js:1860 _milestoneFunction @ Browser.js:1792 loadConfig @ Browser.js:1846 (anonymous) @ Browser.js:73 callback @ ready.js:121 onEvent @ ready.js:47 processQ @ domReady.js:49 detectReady @ domReady.js:62 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#31 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAt2qqBW3ASn-d18cYt7qWj101O_BYRXks5vSneigaJpZM4Y1UaM>.

[nathandunn]

I'm going to close this for now. Moving the original scope to #42

[nathandunn]

But feel free to re-open if still an issue.