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  1. IGB
  2. IGBF-3924

Investigate: Metacerberus .gff output causing error in IGB

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          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:

          1. prodigal_Lambda_phage_sequences.gff
          2. 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

            Attachments

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-3884 Create documentation for MetaCerberus

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed
              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-3927 Investigate: GFF parser error

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                pkulzer Paige Kulzer created issue -
                pkulzer Paige Kulzer made changes -
                Field Original Value New Value
                Epic Link IGBF-2809 [ 19325 ]
                pkulzer Paige Kulzer made changes -
                Link This issue blocks IGBF-3884 [ IGBF-3884 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pkulzer Paige Kulzer made changes -
                Assignee Nowlan Freese [ nfreese ] Paige Kulzer [ pkulzer ]
                pkulzer Paige Kulzer made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                pkulzer Paige Kulzer made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                pkulzer Paige Kulzer made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                pkulzer Paige Kulzer made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                pkulzer Paige Kulzer made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                pkulzer Paige Kulzer made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                pkulzer Paige Kulzer made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                pkulzer Paige Kulzer made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3927 [ IGBF-3927 ]
                nfreese Nowlan Freese made changes -
                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:

                {noformat}
                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)
                {noformat}


                *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                 		*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:

                {noformat}
                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)
                {noformat}


                *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

                  People

                  • Assignee:
                    pkulzer Paige Kulzer
                    Reporter:
                    pkulzer Paige Kulzer
                  • Votes:
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                    Watchers:
                    1 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: