Load Track by URL Fails

[Dario Strbenac]

I use File -> Load from URL ... and paste into the box http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed

I get an error that contains "Unable to parse header with error: File not found"

However, if I paste the URL into Firefox, I see the contents of the BED file. In addition, if I zoom close into a region, I get the DNA bases loaded, and I notice a message

INFO [2013-08-01 18:10:58,652]  [HttpUtils.java:697] [AWT-EventQueue-0]  Range-byte request succeeded

Therefore, IGV appears to be correctly working with the proxy settings I have provided it with.

Additionally, if I do this on my home internet connection it works. What settings should I ask my IT administrator to investigate ? Or, is the Load from URL feature accidentally not using the proxy settings ?

I have IGV 2.3.12.

[Jacob Silterra]

Hi Dario,

IGV 2.3.12 does not use system proxy settings by default (the next version will). If you are behind a proxy, you need to adjust IGVs settings. See http://www.broadinstitute.org/igv/Preferences#Proxy. I can't think of a reason why Load From URL wouldn't use the IGV proxy settings. Can you send your igv.log file? Also, please try out the snapshot build at https://www.broadinstitute.org/software/igv/download_snapshot

Thanks,

-Jacob

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[Dario Strbenac]

I tried the development build, and there was no difference.

INFO [2013-08-05 09:45:32,442] [Main.java:72]  Startup  IGV Version 2.3.12 (14)07/15/2013 11:05 PM
INFO [2013-08-05 09:45:32,443] [Main.java:73]  Java 1.6.0_29
INFO [2013-08-05 09:45:32,443] [Main.java:74]  Default User Directory: C:\Users\Dario\Documents
INFO [2013-08-05 09:45:34,980] [GenomeManager.java:957]  java.io.FileNotFoundException: C:\Users\Dario\igv\genomes\user-defined-genomes.txt (The system cannot find the file specified)
INFO [2013-08-05 09:45:35,006] [GenomeManager.java:117]  Loading genome: http://igv.broadinstitute.org/genomes/hg19.genome
INFO [2013-08-05 09:45:38,049] [GenomeManager.java:161]  Genome loaded.  id= hg19
INFO [2013-08-05 09:45:38,106] [CommandListener.java:81]  Listening on port 60151
INFO [2013-08-05 09:46:12,649] [IGV.java:1553]  Loading 1 resources.
INFO [2013-08-05 09:46:12,684] [TrackLoader.java:115]  Loading resource, path http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed
ERROR [2013-08-05 09:46:12,980] [TrackLoader.java:256]  Unable to parse header with error: File not found: http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed, for input source: http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed
org.broad.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: File not found: http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed, for input source: http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed
    at org.broad.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:127)
    at org.broad.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:81)
    at org.broad.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:69)
    at org.broad.igv.track.TrackLoader.loadFeatureFile(TrackLoader.java:413)
    at org.broad.igv.track.TrackLoader.load(TrackLoader.java:202)
    at org.broad.igv.track.TrackLoader.load(TrackLoader.java:101)
    at org.broad.igv.ui.IGV.load(IGV.java:1660)
    at org.broad.igv.ui.IGV$11.run(IGV.java:1574)
    at org.broad.igv.ui.IGV.loadResources(IGV.java:1587)
    at org.broad.igv.ui.IGV$5.run(IGV.java:673)
    at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:57)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:662)
Caused by: java.io.FileNotFoundException: File not found: http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed
    at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:604)
    at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:505)
    at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:501)
    at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:199)
    at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:193)
    at org.broad.igv.util.stream.IGVUrlHelper.openInputStream(IGVUrlHelper.java:44)
    at org.broad.tribble.util.ParsingUtils.openInputStream(ParsingUtils.java:78)
    at org.broad.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:119)
    ... 15 more
ERROR [2013-08-05 09:46:12,984] [IGV.java:1578]  Error loading track
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed<br>Unable to parse header with error: File not found: http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed, for input source: http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed
    at org.broad.igv.track.TrackLoader.load(TrackLoader.java:257)
    at org.broad.igv.track.TrackLoader.load(TrackLoader.java:101)
    at org.broad.igv.ui.IGV.load(IGV.java:1660)
    at org.broad.igv.ui.IGV$11.run(IGV.java:1574)
    at org.broad.igv.ui.IGV.loadResources(IGV.java:1587)
    at org.broad.igv.ui.IGV$5.run(IGV.java:673)
    at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:57)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:662)
INFO [2013-08-05 09:46:12,988] [MessageUtils.java:60]  Error loading http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed: An error occurred while accessing:    http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed<br>Unable to parse header with error: File not found: http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed, for input source: http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed

[Jim Robinson]

Dario,

Are you still having issues with this?  If so, could you try the latest release?  With respect to the bed file (http://www.maths.usyd.edu.au/u/dario/ProstateCAGE/resources/PrEC.bed),  it apparently does not exist.   I tried this URL in a web browser and got the "file not found" error.

[Dario Strbenac]

Sorry, I moved the file on the server. It's back now. Also, I figured out I was providing the wrong proxy server port. It was set to the HTTPS proxy, not the HTTP proxy. The domain section of the URL for both servers is the same, only the port number differs. Once I fixed it, it was fine.