А почему собственно не закрывается поток - то?

str.charAt(str.length() - 1

if (!reader.ready()){
            try {
                if (str.charAt(str.length() - 1) == ',' && str.length() - 1 != -1)
                    string = str.toString().substring(0, str.length() - 1);
            } catch (StringIndexOutOfBoundsException sie) {
                break;
            }}

package com.javarush.task.task19.task1925;

/*
Длинные слова
*/



import java.io.*;

public class Solution {
    public static void main(String[] args) throws IOException {
        String name1 = args[0];
        String name2 = args[1];
        BufferedReader reader = new BufferedReader(new FileReader(name1));
        BufferedWriter writer = new BufferedWriter(new FileWriter(name2));
        String line = reader.readLine();
        while (line != null) {
            String[] words = line.split(" ");
            StringBuilder str = new StringBuilder();
            for (String word : words) {
                if (word.length() > 6) str.append(word).append(',');
            }
            String string = str.toString();
            if (!reader.ready()){
            try {
                if (str.charAt(str.length() - 1) == ',' && str.length() - 1 != -1)
                    string = str.toString().substring(0, str.length() - 1);
            } catch (StringIndexOutOfBoundsException sie) {
                break;
            }}
            writer.write(string);
            writer.flush();
            line = reader.readLine();
        }
        reader.close();
        writer.close();
    }
}

7777777 7777777
333

public class Solution {
    public static void main(String[] args) {
        try {
            BufferedReader reader = new BufferedReader(new FileReader(args[0]));
            StringBuilder sb = new StringBuilder();

            while (reader.ready()) {
                sb.append(reader.readLine() + "\n");
            }
            reader.close();

            Pattern pattern = Pattern.compile("(?<=(^|\\s))\\S{7,}(?=($|\\s))");
            Matcher matcher = pattern.matcher(sb);
            StringBuilder out = new StringBuilder();

            while (matcher.find()){
                out.append(matcher.group() + ",");
            }

            pattern = Pattern.compile(",$");
            matcher = pattern.matcher(out);
            String s="";

            while (matcher.find()) {
                s = matcher.replaceAll("");
            }
            System.out.println(s);

            BufferedWriter writer = new BufferedWriter(new FileWriter(args[1]));
            writer.write(s);
            writer.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}