java.lang.Exception: FATAL ERROR: SAMRecord is improperly paired! Is the file sorted by name? Offending reads: D00118:263:C89KTANXX:4:1101:1261:94887 != D00118:263:C89KTANXX:4:1101:1262:77904 If the file is not sorted by name then you should included the '--coordSorted' parameter. (Note: in coordSorted mode it is highly recommended but not actually required that the file be sorted by position) This problem could also have a number of other causes: if there are orphaned reads that aren't marked as such in the sam flags, for example.

GitHub | royfrancis | 3 months ago
  1. 0

    Issue with spike-ins

    GitHub | 3 months ago | royfrancis
    java.lang.Exception: FATAL ERROR: SAMRecord is improperly paired! Is the file sorted by name? Offending reads: D00118:263:C89KTANXX:4:1101:1261:94887 != D00118:263:C89KTANXX:4:1101:1262:77904 If the file is not sorted by name then you should included the '--coordSorted' parameter. (Note: in coordSorted mode it is highly recommended but not actually required that the file be sorted by position) This problem could also have a number of other causes: if there are orphaned reads that aren't marked as such in the sam flags, for example.
  2. 0

    GitHub comment 22#247979622

    GitHub | 3 months ago | hartleys
    java.lang.Exception: FATAL ERROR: SAMRecord is improperly paired! Is the file sorted by name? Offending reads: D00118:263:C89KTANXX:4:1101:1261:94887 != D00118:263:C89KTANXX:4:1101:1262:77904 If the file is not sorted by name then you should included the '--coordSorted' parameter. (Note: in coordSorted mode it is highly recommended but not actually required that the file be sorted by position) This problem could also have a number of other causes: if there are orphaned reads that aren't marked as such in the sam flags, for example.
  3. 0

    [SOLVED] My Eclipse is acting up

    minecraftforge.net | 1 year ago
    java.lang.Exception: Illegal ASTNode positions: previousEnd=697, childStart=696, element==Minecraft/C:\/Users\/NovaPC\/.gradle\/caches\/minecraft\/net\/minecraftforge\/forge\/1.8-11.14.2.1430\/snapshot\/20150518\/forgeSrc-1.8-11.14.2.1430.jar<net.minecraftforge.fml.common(Mod.class[Mod, Javadoc: /**  * This defines a Mod to FML.  * Any class found with this annotation applied will be loaded as a Mod. The instance that is loaded will  * represent the mod to other Mods in the system. It will be sent various subclasses of {@link FMLEvent}  * at pre-defined times during the loading of the game, based on where you have applied the {@link EventHandler}  * annotation.  *  * <p>This is a simple example of a Mod. It has the modId of "MyModId", the name of "My example mod", it is  * version 1.0, and depends on FML being loaded.  * <pre>{@code  * package mymod;  * // Declare that this is a mod with modId "MyModId", name "My example mod", version "1.0" and dependency on FML.  * {@literal @}Mod(modId="MyModId",name="My example mod",version="1.0",dependencies="required-after:FML")  * public class MyMod {  *      // Populate this field with the instance of the mod created by FML  *      {@literal @}Instance("MyModId")  *      public MyMod instance;  *  *      // Mark this method for receiving an {@link FMLEvent} (in this case, it's the {@link FMLPreInitializationEvent})  *      {@literal @}EventHandler public void preInit(FMLPreInitializationEvent event)  *      {  *          // Do stuff in pre-init phase (read config, create blocks and items, register them)  *      }  * }  * }  * </pre>  *  * @author cpw  *  */
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  5. 0

    HikariCP detects connectionleak even though all of my code has a call to close method

    Stack Overflow | 2 months ago | JRojo
    java.lang.Exception: Apparent connection leak detected I already checked and made sure all my sql codes has a call to close method. Here's my HikariConfig : private HikariConfig hikariConfig() { HikariConfig config = new HikariConfig(); config.setDriverClassName(CLASS_FOR_NAME); config.setJdbcUrl(HOST); config.setUsername(USER); config.setPassword(PASS); config.addDataSourceProperty("cachePrepStmts", "true"); config.addDataSourceProperty("prepStmtCacheSize", "250"); config.addDataSourceProperty("prepStmtCacheSqlLimit", "2048"); config.setLeakDetectionThreshold(TimeUnit.SECONDS.toMillis(30)); config.setValidationTimeout(TimeUnit.MINUTES.toMillis(1)); config.setMaximumPoolSize(40); config.setMinimumIdle(0); config.setMaxLifetime(TimeUnit.MINUTES.toMillis(2)); // 120 seconds max life time config.setIdleTimeout(TimeUnit.MINUTES.toMillis(1)); // minutes config.setConnectionTimeout(TimeUnit.MINUTES.toMillis(5)); // millis config.setConnectionTestQuery("/* ping */ SELECT 1"); return config; } here's how my queries look like : public ArrayList<LocationType> getLocationTypes() { ArrayList<LocationType> locationTypes = new ArrayList<>(); Connection connection = null; PreparedStatement pstmt = null; ResultSet resultSet = null; try { connection = DataSource.getInstance().getConnection(); pstmt = connection.prepareStatement("SELECT\n" + " location_type_id,\n" + " location_type_name\n" + "FROM tablename;"); resultSet = pstmt.executeQuery(); while (resultSet.next()) { locationTypes.add(new LocationType(resultSet.getInt("location_type_id"), resultSet.getString("location_type_name"))); } } catch (Exception e) { e.printStackTrace(); } finally { if (resultSet != null) try { resultSet.close(); } catch (SQLException e) { } if (pstmt != null) try { pstmt.close(); } catch (SQLException e) { } if (connection != null) try { connection.close(); } catch (SQLException e) { } } return locationTypes; } I've already tried increasing the connectionLeakDetection, max connection and minimum idle but none of that solved the issue. I have read that it could be caused by the machine(low resources) and connections being closed, I think however, none of these causes the issue. I noticed that some long queries in my code are now being detected as connection leak, even though I am not calling their methods. I hope you guys could help. This is the stack trace : at com..database.DataSource.getConnection(DataSource.java:148)
  6. 0

    ClassFormatError

    Google Groups | 2 years ago | Unknown author
    java.lang.Exception: There were class format errors. This is often caused >> by API only jars on the classpath. If you are using maven then you need to >> place these after the CDI unit dependency as 'provided' scope is still >> available during testing.

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    Root Cause Analysis

    1. java.lang.Exception

      FATAL ERROR: SAMRecord is improperly paired! Is the file sorted by name? Offending reads: D00118:263:C89KTANXX:4:1101:1261:94887 != D00118:263:C89KTANXX:4:1101:1262:77904 If the file is not sorted by name then you should included the '--coordSorted' parameter. (Note: in coordSorted mode it is highly recommended but not actually required that the file be sorted by position) This problem could also have a number of other causes: if there are orphaned reads that aren't marked as such in the sam flags, for example.

      at internalUtils.Reporter$.error()
    2. internalUtils
      stdUtils$IteratorProgressReporter$$anon$4.next
      1. internalUtils.Reporter$.error(Reporter.scala:269)
      2. internalUtils.commonSeqUtils$$anon$1.next(commonSeqUtils.scala:682)
      3. internalUtils.commonSeqUtils$$anon$1.next(commonSeqUtils.scala:676)
      4. internalUtils.stdUtils$IteratorProgressReporter$$anon$4.next(stdUtils.scala:302)
      4 frames
    3. Scala
      Iterator$class.foreach
      1. scala.collection.Iterator$class.foreach(Iterator.scala:743)
      1 frame
    4. internalUtils
      stdUtils$IteratorProgressReporter$$anon$4.foreach
      1. internalUtils.stdUtils$IteratorProgressReporter$$anon$4.foreach(stdUtils.scala:296)
      1 frame
    5. qcUtils
      runAllQC$allQC_runner.run
      1. qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1055)
      2. qcUtils.runAllQC$.run(runAllQC.scala:774)
      3. qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:502)
      3 frames
    6. runner
      runner.main
      1. runner.runner$.main(runner.scala:92)
      2. runner.runner.main(runner.scala)
      2 frames