Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:0.5
-
Epic Link:
-
Sprint:Sprint 8
Description
E-mail from Dr. Loraine:
Hi,
I found this in my “drafts” email box and so I’m not sure if you got this update:
Our site at UNC Charlotte that was hosting the data files for the paper crashed. I thought it was being backed up but it turns out not.
I set up a new site for the data files.
It is http://www.bioviz.org/abiotic
Mason - can you help us double-check that everything is working correctly with IGB?
-Ann
Attachments
Activity
I've also examined the Quickload page and it seems like all required BAM index files are present so I'm not sure why the exception is being generated.
While trying to add the first read under Drought --> SM --> Reads --> Wet D, alignments I am getting an exception in the console (see below):
com.affymetrix.genometryImpl.symloader.BAM$BamIndexNotFoundException: Could not find Bam Index File.
at com.affymetrix.genometryImpl.symloader.BAM.findIndexFile(BAM.java:353)
at com.affymetrix.genometryImpl.symloader.BAM.getBamIndexUriStr(BAM.java:100)
at com.affymetrix.genometryImpl.symloader.BAM.getSAMFileReader(BAM.java:80)
at com.affymetrix.genometryImpl.symloader.BAM.init(BAM.java:118)
at com.affymetrix.genometryImpl.symloader.XAM.getChromosomeList(XAM.java:97)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:143)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:130)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:110)
at com.affymetrix.genometryImpl.quickload.QuickloadServerType.loadFeatures(QuickloadServerType.java:382)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:948)
at com.affymetrix.igb.view.load.GeneralLoadUtils$4.runInBackground(GeneralLoadUtils.java:880)
at com.affymetrix.igb.view.load.GeneralLoadUtils$4.runInBackground(GeneralLoadUtils.java:875)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:69)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
I also keep seeing errors when opening IGB (see screenshot "Abiotic-site-errors). However, these errors are not always present.