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:1
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Epic Link:
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Sprint:Fall 2
Description
Situation: Dr. Rick White has asked us to create some documentation for visualizing the output of his program Metacerberus in IGB. I've been working with his student Joshua Hensley to obtain sample output to test in IGB, but currently half of the .gff files being output by the program are throwing errors when they're loaded into IGB.
Here are the first few lines of the error messages:
10:44:46.743 ERROR c.a.genometry.thread.CThreadWorker - class com.affymetrix.genometry.symloader.GFF3 cannot be cast to class com.affymetrix.genometry.quickload.QuickLoadSymLoader (com.affymetrix.genometry.symloader.GFF3 and com.affymetrix.genometry.quickload.QuickLoadSymLoader are in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @2f4b02c6) java.lang.ClassCastException: class com.affymetrix.genometry.symloader.GFF3 cannot be cast to class com.affymetrix.genometry.quickload.QuickLoadSymLoader (com.affymetrix.genometry.symloader.GFF3 and com.affymetrix.genometry.quickload.QuickLoadSymLoader are in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @2f4b02c6) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1041) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1020) at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:305) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317) at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:342) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1583)
Task: Investigate why some of the .gff files output by Metacerberus are throwing errors when being loaded into IGB 10.1.0.
Files which are throwing the above error:
- prodigal_Lambda_phage_sequences.gff
- FragGeneScan_Lambda_phage_sequences.gff
Link to Metacerberus output on Google Drive: https://drive.google.com/drive/folders/14noPsmKYMxX9jgHYQhkjqaTGzT8z8bSK
Link to file on Loraine Lab Google Drive: https://drive.google.com/drive/folders/1MLsVItXNcskfiCAg62GFmxWc1-NR40Tx?usp=drive_link
