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  1. Deep Backlog
  2. DB-80

IGB may fail on unsorted bed files

          Details

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

            Description

            This task was created to serve as a reminder for the story of examining the problem of IGB failing on unsorted bed files.

            There may be a problem with IGB's sorting code that is causing this problem.

            For a related story please see IGBF-490.

            Also, there is an exception that is generated occasionally that may be related to this issue (see comment below for exception).

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                relates to

                Task - A task that needs to be done. IGBF-490 Loading S. cerevisiae genome multiple times causes an exception

                • Major - Major loss of function.
                • Closed

                  Activity

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                  mason Mason Meyer (Inactive) created issue -
                  mason Mason Meyer (Inactive) made changes -
                  Field Original Value New Value
                  Epic Link IGBF-439 [ 15497 ]
                  mason Mason Meyer (Inactive) made changes -
                  Link This issue relates to IGBF-490 [ IGBF-490 ]
                  mason Mason Meyer (Inactive) made changes -
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                  mason Mason Meyer (Inactive) made changes -
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                  mason Mason Meyer (Inactive) added a comment -

                  java.lang.ArrayIndexOutOfBoundsException: 1
                  at com.affymetrix.genometry.util.SortTabFile$LineComparator.minimum(SortTabFile.java:148) ~[genometry-8.3.1.jar:na]
                  at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:117) ~[genometry-8.3.1.jar:na]
                  at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:96) ~[genometry-8.3.1.jar:na]
                  at java.util.TimSort.countRunAndMakeAscending(TimSort.java:356) ~[na:1.8.0_25]
                  at java.util.TimSort.sort(TimSort.java:230) ~[na:1.8.0_25]
                  at java.util.Arrays.sort(Arrays.java:1512) ~[na:1.8.0_25]
                  at java.util.ArrayList.sort(ArrayList.java:1454) ~[na:1.8.0_25]
                  at java.util.Collections.sort(Collections.java:175) ~[na:1.8.0_25]
                  at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:51) ~[genometry-8.3.1.jar:na]
                  at com.affymetrix.genometry.symloader.SymLoader.sortCreatedFiles(SymLoader.java:96) ~[genometry-8.3.1.jar:na]
                  at com.affymetrix.genometry.symloader.BED.init(BED.java:90) ~[genometry-8.3.1.jar:na]
                  at com.affymetrix.genometry.symloader.BED.getChromosomeList(BED.java:98) ~[genometry-8.3.1.jar:na]
                  at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:144) ~[genometry-8.3.1.jar:na]
                  at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:131) ~[genometry-8.3.1.jar:na]
                  at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:111) ~[genometry-8.3.1.

                  Show
                  mason Mason Meyer (Inactive) added a comment - java.lang.ArrayIndexOutOfBoundsException: 1 at com.affymetrix.genometry.util.SortTabFile$LineComparator.minimum(SortTabFile.java:148) ~ [genometry-8.3.1.jar:na] at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:117) ~ [genometry-8.3.1.jar:na] at com.affymetrix.genometry.util.SortTabFile$LineComparator.compare(SortTabFile.java:96) ~ [genometry-8.3.1.jar:na] at java.util.TimSort.countRunAndMakeAscending(TimSort.java:356) ~ [na:1.8.0_25] at java.util.TimSort.sort(TimSort.java:230) ~ [na:1.8.0_25] at java.util.Arrays.sort(Arrays.java:1512) ~ [na:1.8.0_25] at java.util.ArrayList.sort(ArrayList.java:1454) ~ [na:1.8.0_25] at java.util.Collections.sort(Collections.java:175) ~ [na:1.8.0_25] at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:51) ~ [genometry-8.3.1.jar:na] at com.affymetrix.genometry.symloader.SymLoader.sortCreatedFiles(SymLoader.java:96) ~ [genometry-8.3.1.jar:na] at com.affymetrix.genometry.symloader.BED.init(BED.java:90) ~ [genometry-8.3.1.jar:na] at com.affymetrix.genometry.symloader.BED.getChromosomeList(BED.java:98) ~ [genometry-8.3.1.jar:na] at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:144) ~ [genometry-8.3.1.jar:na] at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:131) ~ [genometry-8.3.1.jar:na] at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:111) ~[genometry-8.3.1.
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                  mason Mason Meyer (Inactive) added a comment -

                  When re-enabling a local quickload directory that contained bed files that weren't tabix indexed another exception was generated. (may be a Windows problem):

                  May 06, 2015 2:39:15 PM com.affymetrix.genometry.util.SortTabFile writeFile
                  SEVERE: Could not find file C:\Users\LORAIN~1\AppData\Local\Temp\chr25725627626511728424.bed
                  java.io.FileNotFoundException: C:\Users\LORAIN~1\AppData\Local\Temp\chr25725627626511728424.bed (The requested operation cannot be performed on a file with a user-mapped section open)
                  at java.io.FileOutputStream.open0(Native Method)
                  at java.io.FileOutputStream.open(Unknown Source)
                  at java.io.FileOutputStream.<init>(Unknown Source)
                  at java.io.FileOutputStream.<init>(Unknown Source)
                  at com.affymetrix.genometry.util.SortTabFile.writeFile(SortTabFile.java:79)
                  at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:67)
                  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:782)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$1.loadOnSequence(GeneralLoadUtils.java:697)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$1.lambda$multiThreadedLoad$79(GeneralLoadUtils.java:640)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$1$$Lambda$277/1113018365.run(Unknown Source)
                  at java.util.concurrent.Executors$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)

                  Show
                  mason Mason Meyer (Inactive) added a comment - When re-enabling a local quickload directory that contained bed files that weren't tabix indexed another exception was generated. (may be a Windows problem): May 06, 2015 2:39:15 PM com.affymetrix.genometry.util.SortTabFile writeFile SEVERE: Could not find file C:\Users\LORAIN~1\AppData\Local\Temp\chr25725627626511728424.bed java.io.FileNotFoundException: C:\Users\LORAIN~1\AppData\Local\Temp\chr25725627626511728424.bed (The requested operation cannot be performed on a file with a user-mapped section open) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(Unknown Source) at java.io.FileOutputStream.<init>(Unknown Source) at java.io.FileOutputStream.<init>(Unknown Source) at com.affymetrix.genometry.util.SortTabFile.writeFile(SortTabFile.java:79) at com.affymetrix.genometry.util.SortTabFile.sort(SortTabFile.java:67) 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:782) at com.affymetrix.igb.view.load.GeneralLoadUtils$1.loadOnSequence(GeneralLoadUtils.java:697) at com.affymetrix.igb.view.load.GeneralLoadUtils$1.lambda$multiThreadedLoad$79(GeneralLoadUtils.java:640) at com.affymetrix.igb.view.load.GeneralLoadUtils$1$$Lambda$277/1113018365.run(Unknown Source) at java.util.concurrent.Executors$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)
                  dcnorris David Norris (Inactive) made changes -
                  Assignee John Eckstein [ jeckstein ]
                  mason Mason Meyer (Inactive) made changes -
                  Project IGB [ 10840 ] Deep Backlog [ 11041 ]
                  Key IGBF-547 DB-80
                  Workflow Loraine Lab Workflow [ 15817 ] jira [ 16787 ]

                    People

                    • Assignee:
                      jeckstein John Eckstein (Inactive)
                      Reporter:
                      mason Mason Meyer (Inactive)
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                      Dates

                      • Created:
                        Updated: