Problem with input.readLine()

import java.io.*;
public class HorseMain
     public static void main(String[] args) throws IOException
          //declare the FILENAME
          //the user will later give the FILENAME
          String horseFILENAME;
          //declare the variables to be manipulated
          String name, stable, winner, commentsStewards, commentsJockey, commentsPersonal;
          int rating, race, distance;
          String command;
          //Mastery Factor 9: Parsing a text file or other data stream
          //This will be used to accept the input from the user
          BufferedReader input = new BufferedReader( new InputStreamReader(System.in) );
          System.out.println("\t\t\t\tHORSES");
          System.out.println("Enter the name of the file where the horses are saved:");
          horseFILENAME = input.readLine();
          //calling the HorseFile class
          //the actual argument horseFILENAME will be used to open the file
          HorseFile horse = new HorseFile(horseFILENAME);
          //call the load method to load the contents of the file storing the data
          horse.load();
          //asking for user input
          System.out.println("Please enter one of the given commands");
          System.out.println("\t[a]dd a horse");
          System.out.println("\t[d]elete a horse");
          System.out.println("\t[e]dit details of a horse");
          System.out.println("\t[s]earch for a horse by its name");
          System.out.println("\t[p]rint the details of all the horses in the collection");
          System.out.println("\t[g]et the horses having encountered problems in their last race");
          System.out.println("\t[q]uit the program");
          while (true)     //the system must return true
               System.out.println("Command: ");
               command = input.readLine();
               //using simple if...else selection to determine what action to be taken from command
               //if the user wants to add a horse
               if (command.equals("a"))
                    obtainName(name);
                    //perform search to determine whether this horse already exists
                    //if the horse already exists, message to inform user
                    if (horse.search(name) != null)
                         //message to inform the user that this horse already exists
                         System.out.println(name+ " already exists!");
                    else
                         //obtain the details on the horse
                         obtainStable(stable);
                         obtainRating(rating);
                         obtainRace(race);
                         obtainDistance(distance);
                         obtainWinner(winner);
                         obtainCommentsStewards(commentsStewards);
                         obtainCommentsJockey(commentsJockey);
                         obtainCommentsPersonal(commentsPersonal);
                         //add a new horse record
                         if (!horse.add(name, stable, rating, race, distance, winner, commentsStewards, commentsJockey, commentsPersonal))
                              System.out.println("Sorry");
                              System.out.println(name + " cannot be written to file");
               //if the user wants to delete a horse
               if (command.equals("d"))
                    System.out.println("Enter name of horse to be deleted: ");
                    name = input.readLine();
                    //perform search to determine whether this horse already exists
                    //if horse does exist, horse is deleted
                    if (horse.search(name) != null)
                         horse.delete(name);
                         System.out.println(name + " deleted!");
                    //if horse does not exist, message is output
                    else
                         System.out.println(name + " not found!");
               //if the user wants to edit the details of a horse
               if (command.equals("e"))
                    System.out.println("Enter name of horse to be edited: ");
                    name = input.readLine();
                    //perform search to determine whether this horse already exists
                    //if the horse does exist
                    if (horse.search(name) != null)
                         //obtain the new details of the horse
                         obtainStable(stable);
                         obtainRating(rating);
                         obtainRace(race);
                         obtainDistance(distance);
                         obtainWinner(winner);
                         obtainCommentsStewards(commentsStewards);
                         obtainCommentsJockey(commentsJockey);
                         obtainCommentsPersonal(commentsPersonal);
                         horse.edit(name, stable, rating, race, distance, winner, commentsStewards, commentsJockey, commentsPersonal);
                    //if the horse does not exist
                    else
                         System.out.println(name + "not found in collection");
               //if the user wants to print the details of all the horses
               if (command.equals("p"))
                    horse.display();
               //if the user wants to quit the program
               if (command.equals("q"))
                    break;     //the system exits from the if...else selection
          input.close();
          horse.save();
     /**This is the method to get the name of a horse from the user
     **validation rules: length check
     **The length of a horse name cannot exceed 18 characters.
     public static void obtainName(String name)
          System.out.println("Name of horse: ");
          name = input.readLine();
          //using simple if...else to validate user input
          if (name.length() <= 18)
               //do nothing
          else
               //output error message
               System.out.println("Error! Name should not exceed 18 characters");
               //Using mastery factor recursion to allow the user to input the name again
               obtainName(name);
     /**This is the method to get the stable of a horse from the user
     **No validation rules are used
     **Any string is accepted
     public static void obtainStable(String stable)
          System.out.println("Stable: ");
          stable = input.readLine();
     /**This is the method to get the rating of the horse from the user
     **Validation rules: range check
     **Rating should be between 20 and 110
     public static void obtainRating(int rating)
          System.out.println("Rating: ");
          rating = Integer.parseInt(input.readLine());
          //using multiple if...else selection
          if ( (rating >= 20) && (rating <= 110) )
               //do nothing
          else
               //output error message
               System.out.println("Error! Rating should be between 20 and 110");
               //using mastery factor - recursion - to allow the user to input the rating again
               obtainRating(rating);
     /**This is the method to get the number of the last race run by the horse
     **Validation rules: range check
     **Race number should be between 11 and 308
     public static void obtainRace(int race)
          System.out.println("Race number: ");
          race = Integer.parseInt(input.readLine());
          //using if...else
          if ( (race >= 11) && (race <= 308) )
               //do nothing
          else
               //output error message
               System.out.println("Error! Race number should 11 and 308");
               //using mastery factor - recursion - to allow the user to input the rating again
               obtainRace(race);
     /**This is the method to get the distance of the last race
     **Validation rule: comparison check
     **Distance can either be 1365, 1400, 1500, 1600, 1800, 2000, 2200, 2400
     public static void obtainDistance(int distance)
          System.out.println("Distance: ");
          distance = Integer.parseInt(input.readLine());
          //using if...else
          if ( (distance == 1365) || (distance == 1400) || (distance == 1500) || (distance == 1600) || (distance == 1800) || (distance == 2000) || (distance == 2200) || (distance == 2400) )
               //do nothing
          else
               //output error message
               System.out.println("Error! Distance can either 1365, 1400, 1500, 1600, 1800, 2000, 2200, 2400");
               //using mastery factor recursion to allow the user to input the distance again
               obtainDistance(distance);
     /**This is the method to get the winner of the last race
     **Validation rule: length check
     **The name of the winner cannot exceed 18 characters
     public static void obtainWinner(String winner)
          System.out.println("Winner: ");
          winner = input.readLine();
          //using if...else
          if (winner.length() <= 18)
               //do nothing
          else
               //output error message
               System.out.println("Error! The name of the winner cannot exceed 18 characters");
               //using mastery factor recursion to allow the user to input the winner again
               obtainWinner(winner);
     /**This is the method to get the stewards' comments on a horse
     **No validation rules
     **Any string is accepted
     public static void obtainCommentsStewards(String commentsStewards)
          System.out.println("Stewards' comments: ");
          commentsStewards = input.readLine();
     /**This is the method to get the stewards' comments on a horse
     **No validation rules
     **Any string is accepted
     public static void obtainCommentsJockey(String commentsJockey)
          System.out.println("Jockey's comments: ");
          commentsJockey = input.readLine();
     /**This is the method to get the stewards' comments on a horse
     **No validation rules
     **Any string is accepted
     public static void obtainCommentsPersonal(String commentsPersonal)
          System.out.println("Personal comments: ");
          commentsPersonal = input.readLine();
}

I see one problem already though. You defined "input" as a local variable in your main method, and then refer to it all over the place, outside of the main method.
If you want to use input like that, you'll have to define it as a field, not a local variable.
By the way your code is structured in a kind of hairy way. In OOP you usually want to structure your code around self-contained, encapsulated state and behavior, not just as a bunch of individual actions effecting global variables.

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    To Bnarva for info:
    Here is the package javagently, using "Text":
    package javagently;
    import java.io.*;
    import java.util.*;
    import java.text.*;
    public class Text {
      public Text () {};
      /* The All New Famous Text class     by J M Bishop  Aug 1996
       *            revised for Java 1.1 by Alwyn Moolman Aug 1997
       *            revised for efficiency by J M Bishop Dec 1997
       * Provides simple input from the keyboard and files.
       * Now also has simple output formatting methods
       * and file opening facilities.
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       * public static int    readInt (BufferedReader in)
       * public static double readDouble (BufferedReader in) 
       * public static String readString (BufferedReader in) 
       * public static char   readChar (BufferedReader in)
       * public static String writeInt (int number, int align)
       * public static String writeDouble
                       (double number, int align, int frac)
       * public static BufferedReader open (InputStream in)
       * public static BufferedReader open (String filename)
       * public static PrintWriter create (String filename)
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      private static String S;
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