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
Current task - Quickloads need to be uploaded to reflect the changes to the Lotmaria passim files in the SVN repository.
Tested using lorainelab-quickload.scidas.org
The off by one error is no longer present.
[~aloraine] - igbquickload.org still has the older version of the annotation. Can I close this issue or wait until igbquickload.org has also been updated?
Updated igbquicload.org:
[aloraine@cci-vm12 quickload]$ svn up U L_passim_Apr_2014/CDS_Crithidia.bed.gz.tbi U L_passim_Apr_2014/Exon_Crithidia.bed.gz.tbi U L_passim_Apr_2014/gene_Crithidia.bed.gz.tbi U L_passim_Apr_2014/match_Crithidia.bed.gz U L_passim_Apr_2014/Protein_match_Crithidia.bed.gz U L_passim_Apr_2014/mRNA_Crithidia.bed.gz U L_passim_Apr_2014/Expressed_sequence_match_Crithidia.bed.gz U L_passim_Apr_2014/CDS_Crithidia.bed.gz U L_passim_Apr_2014/Exon_Crithidia.bed.gz U L_passim_Apr_2014/Protein_match_Crithidia.bed.gz.tbi U L_passim_Apr_2014/match_Crithidia.bed.gz.tbi U L_passim_Apr_2014/mRNA_Crithidia.bed.gz.tbi U L_passim_Apr_2014/gene_Crithidia.bed.gz U L_passim_Apr_2014/Expressed_sequence_match_Crithidia.bed.gz.tbi Updated to revision 148.
Same at "renci" quickload.
Updated. Moving to "Needs Testing"
I am able to open and run ProtAnnot without the reported errors. Tested on macOS.
To replicate the issue in IGB:
1) Select the Lotmaria passim genome in the Species menu and the L_passim_Apr_2014 Genome Version.
2) Navigate to Contig_1:81,219-95,810
3) Install ProtAnnot: Plug-ins > Launch App Manager > ProtAnnot > click Install
4) In IGB, select the gene in view.
5) Select Tools > Start ProtAnnot