TRF on the scanning stage when kicked for chr1

[ds-gene104]

I ran trf for all the chromosomes separately for which I got results in no time but for chr1 it didnt move ahead in the scanning stage.... I am using trf v4.09 and the size of the file is 300 mbs.... I kicked it off earlier on thursday meaning it ran for almost 4-5 days, then a second run on monday specifying parameters like -l = 6 and -fdh... two other chromosomes didn't generate the .dat files which were chr12 and chrX, for which I used -l =6 and it generated the output in a few minutes

the two commands I used for chr1 are:

1. trf chr1.fasta 2 7 7 80 10 50 500 -l 6 -fdh 2> chr1_3_35.log
2. trf chr1.fasta 2 7 7 80 10 50 500 -fdh 2> chr1_3_39.log

this is what I can see in the log file:

~
~
~

Tandem Repeats Finder, Version 4.09
Copyright (C) Dr. Gary Benson 1999-2012. All rights reserved.

Loading sequence...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning...
(END)

I would be truly grateful if there is a solution for this

Thank you.