[EMBOSS] size limits on extractseq?

[Iain Drummond]

Is there an upper limit on the file size that extractseq can handle?

I run into a problem using extractseq to get segments out of mouse
chromosome files. It will only access the first 19.7 MB or so of a 185 MB
file. The files are fasta files of the mouse genome build 32 from NCBI. Here
is what the problem looks like: (real file sizes are ls'd below)

$ extractseq
Extract regions from a sequence
Input sequence: mm_chr1.fa
Regions to extract (eg: 4-57,78-94) [1-19589943]:
 
$ extractseq
Extract regions from a sequence
Input sequence: mm_chr2.fa
Regions to extract (eg: 4-57,78-94) [1-19704910]:
 
$ ls -l
total 3782918
-rw-r--r--   1 nobody   nobody   200460727 May 25 23:56 mm_chr1.fa
-rw-r--r--   1 nobody   nobody   135604265 May 26 15:16 mm_chr10.fa
-rw-r--r--   1 nobody   nobody   123799904 May 26 15:17 mm_chr11.fa
-rw-r--r--   1 nobody   nobody   120032577 May 26 15:19 mm_chr12.fa
-rw-r--r--   1 nobody   nobody   119608375 May 26 15:20 mm_chr13.fa
-rw-r--r--   1 nobody   nobody   185168052 May 26 14:28 mm_chr2.fa

-- 

Iain Drummond, Ph.D.
Assistant Professor
Department of Medicine, Harvard Medical School and
Renal Unit, Massachusetts General Hospital

Mailing address:
Renal Unit / MGH 149-8000
149 13th St. 
Charlestown, MA 02129

Tel: 617 726 5647
Fax: 617 726 5669

idrummond at partners.org
idrummon at receptor.mgh.harvard.edu

Lab Home Page:
http://danio.mgh.harvard.edu