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  1. Deep Backlog
  2. DB-192

BGZipped files may need Tabix Index file; examine ways to improve

    Details

    • Type: Bug
    • Status: Open (View Workflow)
    • Priority: Major
    • Resolution: Unresolved
    • Labels:
      None

      Description

      It seems that some BGZipped files may need Tabix Index files for IGB to properly open the complete file. We should examine ways to improve this.

      David's seems to think that it is not a problem with our parser but rather a problem in the way the SamTools library handles BGzipped files that do not have associated tabix index files (ask David for clarification).

      See below for am exception that can arise when this problem happens:

      May 13, 2015 1:28:58 PM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
      WARNING: For input string: "AT4G12610.1"
      java.lang.NumberFormatException: For input string: "AT4G12610.1"
      at java.lang.NumberFormatException.forInputString(Unknown Source)
      at java.lang.Integer.parseInt(Unknown Source)
      at java.lang.Integer.valueOf(Unknown Source)
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.minimum(SortTabFile.java:148)
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:120)
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:99)
      at java.util.TimSort.countRunAndMakeAscending(Unknown Source)
      at java.util.TimSort.sort(Unknown Source)
      at java.util.Arrays.sort(Unknown Source)
      at java.util.ArrayList.sort(Unknown Source)
      at java.util.Collections.sort(Unknown Source)
      at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:54)
      at com.affymetrix.genometry.symloader.SymLoader.sortCreatedFiles(SymLoader.java:109)
      at com.affymetrix.genometry.symloader.BED.init(BED.java:97)
      at com.affymetrix.genometry.symloader.BED.getChromosomeList(BED.java:104)
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:152)
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:138)
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:118)
      at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:783)
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1.loadOnSequence(GeneralLoadUtils.java:698)
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1.lambda$multiThreadedLoad$81(GeneralLoadUtils.java:641)
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1$$Lambda$277/1623074565.run(Unknown Source)
      at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
      at java.util.concurrent.FutureTask.run(Unknown Source)
      at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
      at java.lang.Thread.run(Unknown Source)

      13:28:58.331 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded TAIR10 mRNA in 937.5 ms
      13:28:58.337 ERROR c.a.igb.view.load.GeneralLoadUtils - Error in loadOnSequence
      java.lang.NumberFormatException: For input string: "AT4G12610.1"
      at java.lang.NumberFormatException.forInputString(Unknown Source) ~[na:1.8.0_40]
      at java.lang.Integer.parseInt(Unknown Source) ~[na:1.8.0_40]
      at java.lang.Integer.valueOf(Unknown Source) ~[na:1.8.0_40]
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.minimum(SortTabFile.java:148) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:120) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:99) ~[genometry-8.4.0.jar:na]
      at java.util.TimSort.countRunAndMakeAscending(Unknown Source) ~[na:1.8.0_40]
      at java.util.TimSort.sort(Unknown Source) ~[na:1.8.0_40]
      at java.util.Arrays.sort(Unknown Source) ~[na:1.8.0_40]
      at java.util.ArrayList.sort(Unknown Source) ~[na:1.8.0_40]
      at java.util.Collections.sort(Unknown Source) ~[na:1.8.0_40]
      at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:54) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.symloader.SymLoader.sortCreatedFiles(SymLoader.java:109) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.symloader.BED.init(BED.java:97) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.symloader.BED.getChromosomeList(BED.java:104) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:152) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:138) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:118) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:783) ~[igb-8.4.0.jar:na]
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1.loadOnSequence(GeneralLoadUtils.java:698) [igb-8.4.0.jar:na]
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1.lambda$multiThreadedLoad$81(GeneralLoadUtils.java:641) [igb-8.4.0.jar:na]
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1$$Lambda$277/1623074565.run(Unknown Source) [igb-8.4.0.jar:na]
      at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) [na:1.8.0_40]
      at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.8.0_40]
      at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.8.0_40]
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.8.0_40]
      at java.lang.Thread.run(Unknown Source) [na:1.8.0_40]
      May 13, 2015 1:28:58 PM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
      WARNING: For input string: "ATCYSC1|ARATH;BSAS3;1|CYSC1"
      java.lang.NumberFormatException: For input string: "ATCYSC1|ARATH;BSAS3;1|CYSC1"
      at java.lang.NumberFormatException.forInputString(Unknown Source)
      at java.lang.Integer.parseInt(Unknown Source)
      at java.lang.Integer.valueOf(Unknown Source)
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.minimum(SortTabFile.java:147)
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:120)
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:99)
      at java.util.TimSort.countRunAndMakeAscending(Unknown Source)
      at java.util.TimSort.sort(Unknown Source)
      at java.util.Arrays.sort(Unknown Source)
      at java.util.ArrayList.sort(Unknown Source)
      at java.util.Collections.sort(Unknown Source)
      at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:54)
      at com.affymetrix.genometry.symloader.SymLoader.sortCreatedFiles(SymLoader.java:109)
      at com.affymetrix.genometry.symloader.BED.init(BED.java:97)
      at com.affymetrix.genometry.symloader.BED.getChromosomeList(BED.java:104)
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:152)
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:138)
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:118)
      at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:783)
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1.loadOnSequence(GeneralLoadUtils.java:698)
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1.lambda$multiThreadedLoad$81(GeneralLoadUtils.java:641)
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1$$Lambda$277/1623074565.run(Unknown Source)
      at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
      at java.util.concurrent.FutureTask.run(Unknown Source)
      at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
      at java.lang.Thread.run(Unknown Source)

      13:28:58.886 ERROR c.a.igb.view.load.GeneralLoadUtils - Error in loadOnSequence
      java.lang.NumberFormatException: For input string: "ATCYSC1|ARATH;BSAS3;1|CYSC1"
      at java.lang.NumberFormatException.forInputString(Unknown Source) ~[na:1.8.0_40]
      at java.lang.Integer.parseInt(Unknown Source) ~[na:1.8.0_40]
      at java.lang.Integer.valueOf(Unknown Source) ~[na:1.8.0_40]
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.minimum(SortTabFile.java:147) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:120) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:99) ~[genometry-8.4.0.jar:na]
      at java.util.TimSort.countRunAndMakeAscending(Unknown Source) ~[na:1.8.0_40]
      at java.util.TimSort.sort(Unknown Source) ~[na:1.8.0_40]
      at java.util.Arrays.sort(Unknown Source) ~[na:1.8.0_40]
      at java.util.ArrayList.sort(Unknown Source) ~[na:1.8.0_40]
      at java.util.Collections.sort(Unknown Source) ~[na:1.8.0_40]
      at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:54) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.symloader.SymLoader.sortCreatedFiles(SymLoader.java:109) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.symloader.BED.init(BED.java:97) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.symloader.BED.getChromosomeList(BED.java:104) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:152) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:138) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:118) ~[genometry-8.4.0.jar:na]
      at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:783) ~[igb-8.4.0.jar:na]
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1.loadOnSequence(GeneralLoadUtils.java:698) [igb-8.4.0.jar:na]
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1.lambda$multiThreadedLoad$81(GeneralLoadUtils.java:641) [igb-8.4.0.jar:na]
      at com.affymetrix.igb.view.load.GeneralLoadUtils$1$$Lambda$277/1623074565.run(Unknown Source) [igb-8.4.0.jar:na]
      at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) [na:1.8.0_40]
      at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.8.0_40]
      at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.8.0_40]
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.8.0_40]
      at java.lang.Thread.run(Unknown Source) [na:1.8.0_40]

        Attachments

          Activity

          mason Mason Meyer (Inactive) created issue -
          mason Mason Meyer (Inactive) made changes -
          Field Original Value New Value
          Epic Link IGBF-497 [ 15559 ]
          ann.loraine Ann Loraine made changes -
          Story Points 0.5
          ann.loraine Ann Loraine made changes -
          Project IGB [ 10840 ] Deep Backlog [ 11041 ]
          Key IGBF-653 DB-192
          Workflow Loraine Lab Workflow [ 15935 ] jira [ 16899 ]

            People

            • Assignee:
              Unassigned
              Reporter:
              mason Mason Meyer (Inactive)
            • Votes:
              0 Vote for this issue
              Watchers:
              1 Start watching this issue

              Dates

              • Created:
                Updated: