memory problem

The matlab code below was used to search the contents of File2 with the contents of file1, and with the example output below. However, when large files are involved, the output is reduced.

    File1:
M1U152S44906X14127_xu
M1U7S112336U117688_xu

    File2 (tab delimited):
T1X19S17508N179711_xu  AAU_779
M1U152S44906X14127_xu  xcup
M1U7S112336U117688_xu  mmna

    Expected output:
M1U152S44906X14127_xu  xcup
M1U7S112336U117688_xu  mmna

Code:

 clear all;
clc;
%Open flux file for reading
fid  = fopen('File2.txt')
if fid ==-1
 disp('Reaction_Flux file open not successful')
else    
% Read characters and numbers into separate elements
% in a cell array
 rxn_flux = [];
 A = [];
 B = [];
 C = [];
 rxn_flux = textscan(fid,'%d %s %s');
 A = rxn_flux{1};
 B = rxn_flux{2};
 C = rxn_flux{3};
 len1 = length(B);
   closeresult1 = fclose(fid);
if closeresult1 == 0
         disp('Reaction_Flux file close successful')
     else
         disp('Reaction_Flux file close not successful')
     end
end 
%Open reaction file for reading
fid  = fopen('File1.txt')
if fid ==-1
   disp('Flux file open not successful')
else
 % Read characters and numbers into separate elements
% in a cell array
[rxn] = textread('File1.txt','%s');
%rxn = textscan(fid,'%s');
D = rxn;
len2 = length(D);
closeresult2 = fclose(fid);
if closeresult2 == 0
         disp('Reaction file close successful')
     else
         disp('Reaction file close not successful')
     end
end 
%Open output file for writing results
fid = fopen('OutputFile.txt','w');
fprintf(fid,'The following were found in File 1:\n')
RXNFLUX = false(size(B));
for i = 1:len2
  RXNFLUX = RXNFLUX | strcmpi(D{i},B);
end  
if any(RXNFLUX)
   iLines = [];
   iLines = find(RXNFLUX);
   for i=1:size(iLines)
      fprintf(fid,'%s\t, %s\n',B{iLines(i)}, C{iLines(i)});
      % B{iLines(i)} and C{iLines(i)}
      %fprintf(fid,'%s\t, %s\n', B, C);
      %fprintf(fid, '%s\n', B{:});
      %dlmwrite('output.txt',B(iLines(i)),'\n');
   end
else
  disp('rxn not found')
end
fclose(fid);

I will be happy to get some help to resolve the problem.

Thanks

[per isakson]

Does the full content of File1 and File2 fit i memory at the same time? How large are they?

[Jason Ross]

Can you add:

Operating system

32 bit vs. 64 bit

Amount of RAM in your system

Version of MATLAB

Amount of free memory at start (e.g. run the "memory" command)