The best result with no lookup tables/simd/threads(108mcycles)
#include "void.h" //gist.github.com/FrozenVoid/87e6ad6212ac9ce496e0#file-void-h"
STDSTART
#define dmask(c) dmasku8(((u8)c))
#define dmasku8(c) (c+(c<<8)+(c<<16)+(c<<24)+(c<<32)+(c<<40)+(c<<48)+(c<<56))
#define modz255(x) sm u8 c=(x);u8 dv=(c/255);c-((dv<<8)-dv) em
const u8 inverse0div= ((~(0ULL))/255ULL);
#define inv0mul(x) (inverse0div*(127+(x)))
#define xmaskinv(x) ((x)&(inverse0div*127))
#define countless(x,n) \
(((( inv0mul(n)-xmaskinv(x) )&(~(x))&(inverse0div<<7))/128)%255ULL)
#define dcless(x,n) ((( inv0mul(n)-xmaskinv(x) )&(~(x))&(inverse0div<<7))>>7)
//count 0s
#define dnacount(xh,ms1,ms2) ((dcless((xh^ms1),1)+dcless((xh^ms2),1))) %255
#define dnacount2(xh,ms1,ms2) sm u8 mk1=xh^ms1;u8 mk2=xh^ms2;\
u8 inv0m=inv0mul(1);\
(((( inv0m-xmaskinv(mk1) )&(~(mk1))&(inverse0div<<7))>>7)+((( inv0m-xmaskinv(mk2) )&(~(mk2))&(inverse0div<<7))>>7) )%255 \
em
#define dnacount3(xh,ms1,ms2) sm u8 inv0d=inverse0div<<7;\
u8 inv0m=inv0mul(1);\
modz255(((( inv0m-xmaskinv(xh^ms1) )&(inv0d))>>7)+((( inv0m-xmaskinv(xh^ms2) )&(inv0d))>>7) ) \
em
#define dnacountfunc dnacount3
u8 i=0,j;u8 countGC=0,countTA=0;f8 res;;u1 p;
if(argc<2)quit("No args");u8 fsize=filesize(argv[1]);
if(!fsize)quit("Invalid file");u1p in=filecontent(argv[1]);
//file load speed is dependent on hardware(SSD brands/HDD location in the disk)
u8 st=tsc();for(in[i]=='>';in[i]!='\n';i++);;
while((u8)(&in[i])%8){
countGC+=((in[i]=='G')|(in[i]=='C'));
countTA+=((in[i]=='T')|(in[i]=='A'));i++;}
//8byte chunks MAINLOOP (1thread)
u8 n=i/8,nmax=(fsize/8); u8p inp=(u8p)in;
for( n=i/8;n<nmax;n++){
countGC+=dnacountfunc(inp[n],dmask('G'),dmask('C'));
countTA+=dnacountfunc(inp[n],dmask('T'),dmask('A'));}
for(u8 i=n*8;i<fsize;i++){p=in[i];
countGC+=!((p!='G')&(p!='C'));
countTA+=!((p!='T')&(p!='A')); }
res=((f8)countGC)/(((f8)countGC)+((f8)countTA));
u8 et=tsc();
p("Found GC/GCTA ratio:",res," of file",argv[1],
" in ",et-st,"cycles\n GC:",countGC," TA:",countTA);
/* Found GC/GCTA ratio: 0.376217301393862 of file Homo_sapiens.GRCh37.67.dna_rm.
chromosome.Y.fa in 108865000 cycles
GC: 3228502 TA: 5352980 */ STDEND