PHP : Associative array indexing issue

My problem is very specific. I'm a beginner php programmer and I'm having difficulty indexing the array datastructure in PHP. The program is reading from an input file (input.txt) and storing the result into an array with key same as the item. Although the input.txt files have numbers for convenience I have to store them as string ( My program needs integers of size greater than 32 bit). But when I try to index them as $a["3"] I get an error Undefined offset: 3. I tried $a['3'], $a[3] all with the same result. But curiously I am able to index last element in the array that is $a["2"] correctly! Please help.

Here is the input text file :

3
4
5
1
2

Here is the code segment :

<?php
    ignore_user_abort(true);
    set_time_limit(0);
    $temp=0;
    $a= array();
    $file= fopen("input.txt","r") or exit( "unable to open file");
    while(!feof($file)){
        $temp=fgets($file); 
        $a[$temp]=$temp;     
    }   
    fclose($file);
    echo "<br>The array is .. ";
    foreach ($a as $key => $item) {
        echo "<br> Key => item =",$key."=>",$item ;
        echo "<br>Manual array test ",$a["3"]; // This line demonstrates the problem. 
    }
    echo "<br>Manual array test ",$a["2"]; // This one has no error! So basically only the last element is being indexed correctly

    //echo "<br> No of 2 sums is ",twoSum($a,4,6);
?>