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:
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Story Points:1
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Epic Link:
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Sprint:Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5
Description
Situation: ProtAnnot fails to load the Lotmaria passim genes. There is an error in the console (see below).
Task: Investigate why this error is occurring.
Note: The Lotmaria passim was previously called Crithidia. There may be issues with the annotation files themselves - this may not be a ProtAnnot issue.
12:17:36.184 INFO c.a.igb.view.load.GeneralLoadUtils - All residues in range are already loaded on sequence Contig_1
ERROR: Sequence string passed to DNAUtils.translate() is empty
12:17:36.186 ERROR c.a.genometry.thread.CThreadWorker - com.affymetrix.genometry.span.SimpleSeqSpan cannot be cast to com.affymetrix.genometry.MutableSeqSpan
java.lang.ClassCastException: com.affymetrix.genometry.span.SimpleSeqSpan cannot be cast to com.affymetrix.genometry.MutableSeqSpan
at com.affymetrix.genometry.util.SeqUtils.transformLeafSymmetry(SeqUtils.java:785) ~[na:na]
at com.affymetrix.genometry.util.SeqUtils.transformSymmetry(SeqUtils.java:668) ~[na:na]
at com.affymetrix.genometry.util.SeqUtils.transformSymmetry(SeqUtils.java:602) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.processCDS(ProtannotParser.java:572) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.processMRNA(ProtannotParser.java:525) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.processDNASeq(ProtannotParser.java:399) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.parse(ProtannotParser.java:232) ~[na:na]
at org.lorainelab.igb.protannot.ProtAnnotAction.load(ProtAnnotAction.java:731) ~[na:na]
at org.lorainelab.igb.protannot.ProtAnnotAction$2.runInBackground(ProtAnnotAction.java:262) ~[na:na]
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) ~[na:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_241]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_241]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_241]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_241]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_241]
at java.lang.Thread.run(Thread.java:748) [na:1.8.0_241]
Attachments
Issue Links
- relates to
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IGBF-1360 Fix genome sequence loading for Quickload L_passim_Apr_2014
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Rank | Ranked higher |
| Sprint | Fall 4 Oct 26 - Nov 6 [ 107 ] | |
| Labels | Beginner |
| Summary | Investigate Protannot fail to load Lotmaria passim genes | Investigate ProtAnnot fail to load Lotmaria passim genes |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] | Nowlan Freese [ nfreese ] |
| Sprint | Fall 4 Oct 26 - Nov 6 [ 107 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20 [ 107, 108 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Post-merge Testing In Progress [ 10003 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20 [ 107, 108 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 23 - Dec 4 [ 107, 108, 109 ] |
| Rank | Ranked higher |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11 [ 107, 108, 109 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 107, 108, 109, 110 ] |
| Rank | Ranked higher |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 107, 108, 109, 110 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 107, 108, 109, 110, 111 ] |
| Rank | Ranked higher |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 107, 108, 109, 110, 111 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 107, 108, 109, 110, 111, 112 ] |
| Rank | Ranked higher |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 107, 108, 109, 110, 111, 112 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5 [ 107, 108, 109, 110, 111, 112, 113 ] |
| Rank | Ranked higher |
| Assignee | Irvin Naylor [ inaylor ] |
| Attachment | console1.PNG [ 15134 ] |
| Assignee | Irvin Naylor [ inaylor ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5 [ 107, 108, 109, 110, 111, 112, 113 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19 [ 107, 108, 109, 110, 111, 112, 113, 114 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19 [ 107, 108, 109, 110, 111, 112, 113, 114 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 107, 108, 109, 110, 111, 112, 113, 114, 115 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Philip Badzuh [ pbadzuh ] | Nowlan Freese [ nfreese ] |