Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:0.5
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Epic Link:
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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
| Field | Original Value | New Value |
|---|---|---|
| Sprint | Sprint 5 [ 10 ] |
| Rank | Ranked higher |
| Assignee | David Norris [ dcnorris ] | Mason Meyer [ mason ] |
| Status | Open [ 1 ] | Testing In Progress [ 10003 ] |
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.
| Sprint | Sprint 5 [ 10 ] |
| Sprint | Sprint 6 [ 11 ] |
| Rank | Ranked higher |
| Epic Link | IGBF-236 [ 15233 ] |
| Attachment | Abiotic_site_errors.PNG [ 12852 ] |
I also keep seeing errors when opening IGB (see screenshot "Abiotic-site-errors). However, these errors are not always present.
| Assignee | Mason Meyer [ mason ] | Ann Loraine [ aloraine ] |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Rank | Ranked higher |
| Story Points | 0.5 |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Sprint 6 [ 11 ] |
| Sprint | Sprint 7 [ 12 ] |
| Rank | Ranked higher |
| Sprint | Sprint 7 [ 12 ] |
| Sprint | Sprint 8 [ 13 ] |
| Rank | Ranked higher |
| Status | Reopened [ 4 ] | In Progress [ 3 ] |
| Resolution | Done [ 10000 ] | |
| Status | In Progress [ 3 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 15433 ] | Fall 2019 Workflow Update [ 19233 ] |
| Workflow | Fall 2019 Workflow Update [ 19233 ] | Revised Fall 2019 Workflow Update [ 21350 ] |
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)