paste command in bash doesn't append to end of file

Question

One file has 3 columns and looks like this:

1   249250621   225280621   
2   243199373   238207373   
3   198022430   194797140   
4   191154276   187661676   
5   180915260   177695260   
6   171115067   167395067   
7   159138663   155353663   
8   146364022   142888922   
9   141213431   120143431   
10  135534747   131314747   
11  135006516   131129516   
12  133851895   130481895   
13  115169878   95589878    
14  107349540   88289540    
15  102531392   81694769    
16  90354753    78884753    
17  81195210    77795210    
18  78077248    74657248    
19  59128983    55808983    
20  63025520    59505520    
21  48129895    35108702    
22  51304566    34894566    
X   155270560   151100560   
Y   59373566    25653566    

My other file looks like:

5677533
4506000
2272564
2753699
4015846
2163243
3812595
2885199
8064159
3522086
2006115
1490517
1072244
1423429
3009679
2705191
1479591
800436
929876
648000
347993
972862
7812943
9660863

When I try

paste file1.txt file2.txt > file3.txt

I get:

1   567753321   225280621   
2   450600073   238207373   
3   227256430   194797140   
4   275369976   187661676   
5   401584660   177695260   
6   216324367   167395067   
7   381259563   155353663   
8   288519922   142888922   
9   806415931   120143431   
10  352208647   131314747   
11  200611516   131129516   
12  149051795   130481895   
13  107224478   95589878    
14  142342940   88289540    
15  300967992   81694769    
16  27051913    78884753    
17  14795910    77795210    
18  80043648    74657248    
19  92987683    55808983    
20  64800020    59505520    
21  34799395    35108702    
22  97286266    34894566    
X   781294360   151100560   
Y   96608636    25653566

The data from file2.txt overwrites the 2nd column in file 1. I want the data in file2.txt to be appended to the end in a new column, separated by a tab in file1.txt into the new file3.txt. But it does not seem to be working. Thoughts? Thanks.

Edit: For file2, I can create it with the same first column index 1-22, x, y. But then when I try to join, it doesn't work either. This is my output on join:

1 249250621 225280621
 5677533
2 243199373 238207373
 4506000
3 198022430 194797140
 2272564
4 191154276 187661676
 2753699
5 180915260 177695260
 4015846
6 171115067 167395067
 2163243
7 159138663 155353663
 3812595
8 146364022 142888922
 2885199
9 141213431 120143431
 8064159
10 135534747 131314747
 3522086
11 135006516 131129516
 2006115
12 133851895 130481895
 1490517
13 115169878 95589878
 1072244
14 107349540 88289540
 1423429
15 102531392 81694769
 3009679
16 90354753 78884753
 2705191
17 81195210 77795210
 1479591
18 78077248 74657248
 800436
19 59128983 55808983
 929876
20 63025520 59505520
 648000
21 48129895 35108702
 347993
22 51304566 34894566
 972862
X 155270560 151100560
 7812943
Y 59373566 25653566 9660863

Answer 1

Try running dos2unix on both file1.txt and file2.txt first.

==> dos2unix file*.txt
file1.txt: done.
file2.txt: done.
==> paste file1.txt file2.txt > file3.txt
==> cat file3.txt
1   249250621   225280621       5677533
2   243199373   238207373       4506000
3   198022430   194797140       2272564
4   191154276   187661676       2753699
5   180915260   177695260       4015846
6   171115067   167395067       2163243
7   159138663   155353663       3812595
8   146364022   142888922       2885199
9   141213431   120143431       8064159
10  135534747   131314747       3522086
11  135006516   131129516       2006115
12  133851895   130481895       1490517
13  115169878   95589878        1072244
14  107349540   88289540        1423429
15  102531392   81694769        3009679
16  90354753    78884753        2705191
17  81195210    77795210        1479591
18  78077248    74657248        800436
19  59128983    55808983        929876
20  63025520    59505520        648000
21  48129895    35108702        347993
22  51304566    34894566        972862
X   155270560   151100560       7812943
Y   59373566    25653566        9660863