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aidenlab / Juicebox

Visualization and analysis software for Hi-C data -
https://aidenlab.org/juicebox
MIT License
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large bed file loading error #339

Closed sa501428 closed 5 years ago

sa501428 commented 8 years ago

On Frankenstein with 20GB RAM initialization

INFO [2016-03-02 14:29:41,491] [GenomeManager.java:130] [pool-1-thread-1] Loading genome: http://igvdata.broadinstitute.org/genomes/mm9.genome INFO [2016-03-02 14:29:41,512] [HttpUtils.java:1050] [pool-1-thread-1] Downloading http://igvdata.broadinstitute.org/genomes/mm9.genome to /home/mshamim/igv/genomes/mm9.genome INFO [2016-03-02 14:29:42,839] [HttpUtils.java:1091] [pool-1-thread-1] Download complete. Total bytes downloaded = 2918493 INFO [2016-03-02 14:29:43,679] [GenomeManager.java:174] [pool-1-thread-1] Genome loaded. id= mm9 ERROR [2016-03-02 14:29:43,687] [HiCTrackManager.java:185] [pool-1-thread-1] Error loading track: /media/mshamim/Lavery_Backup/ZoghbiLab/HiC_Feb2016/RNA_Seq/Wooi/bedfile1/file1_chr2.bed java.lang.RuntimeException: IGV has not been initialized. Must call createInstance(Frame) first at org.broad.igv.ui.IGV.getInstance(IGV.java:172) at org.broad.igv.ui.IGV.getMainFrame(IGV.java:199) at org.broad.igv.track.TribbleFeatureSource.createIndex(TribbleFeatureSource.java:107) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:77) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:60) at juicebox.track.HiCTrackManager.loadTribbleFile(HiCTrackManager.java:308) at juicebox.track.HiCTrackManager.loadTrack(HiCTrackManager.java:179) at juicebox.track.HiCTrackManager.unsafeLoad(HiCTrackManager.java:104) at juicebox.track.HiCTrackManager.access$200(HiCTrackManager.java:52) at juicebox.track.HiCTrackManager$2.run(HiCTrackManager.java:95) at juicebox.MainWindow$3.call(MainWindow.java:189) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)

sa501428 commented 5 years ago

bigbed should be used for big bed files