Details
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Type:
Bug
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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:0.25
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Epic Link:
Description
The sequence of the Lotmaria passim genome cannot be loaded.
I discovered this when I tried to run ProtAnnot on an annotation from this genome. ProtAnnot just seemed to hang half open.
When I try to load the sequence for the first chromosome, I get an error message saying
Couldn't locate partial sequence.
This is the same error message I encountered in issue IGBF-1356.
The task here is to determine if the IGBF-1356 issue is the cause here.
>>If fixing that issue will fix this, increase the priority level for that issue because there is at least one genome currently affected by it.
>>If that is not the root cause here, find out what is and create a jira issue to address it.
Either way, it would also be good to check a few other genomes to see which/how many are affected.
Attachments
Issue Links
- relates to
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IGBF-2583 Investigate ProtAnnot fail to load Lotmaria passim genes
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- Closed
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Activity
Is this now fixed?
Someone renamed the .2bit file to L_passim_Apr_2014.2bit in the quickload and scidas. I can load the sequence file for Lotmaria passim in IGB 9.0.2.
When loading protannot, I am getting the following error and nothing is loading in ProtAnnot:
15:04:11.079 INFO c.a.igb.view.load.GeneralLoadUtils - All residues in range are already loaded on sequence Contig_2
ERROR: Sequence string passed to DNAUtils.translate() is empty
15:04:11.081 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:709) ~[na:na]
at com.affymetrix.genometry.util.SeqUtils.transformSymmetry(SeqUtils.java:592) ~[na:na]
at com.affymetrix.genometry.util.SeqUtils.transformSymmetry(SeqUtils.java:526) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.processCDS(ProtannotParser.java:575) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.processMRNA(ProtannotParser.java:528) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.processDNASeq(ProtannotParser.java:402) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.parse(ProtannotParser.java:235) ~[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$1.call(SwingWorker.java:295) [na:1.8.0_192]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_192]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_192]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_192]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_192]
at java.lang.Thread.run(Thread.java:748) [na:1.8.0_192]
ProtAnnot (and IGB?) appear to be failing to recognize the 2bit file as having sequence data for the genome.
The current name in IGB is correct: L_passim_Apr_2014
Crithidia mellificae, strain SF was renamed to Lotmaria passim, strain SF.
To avoid confusion amongst users, a user asked David and I to update the name while also providing synonyms to the previous name (Crithidia). We updated the synonyms file to reflect the name change, but left all of the annotation/sequence files as Crithidia.
Please add:
- IGB name of genome assembly
- Link to genome assembly directory in IGBQuickload.org
Able to load the sequence for L_passim_Apr_2014 in Master 9.1.6 on Mac.
There is a separate issue regarding ProtAnnot failing to load gene models. I have created a new issue
IGBF-2583.Closing issue.