using custom glf instead of angsd output

[fgvieira]

using custom glf instead of angsd output

[fgvieira]

What is the size, in bytes, of the my.glf file?

[LZeitler]

3982711872 bytes

[fgvieira]

Without looking at the files it is difficult, but it seems your GLF file might not be complete. The GLF file should have a size in bytes of = n_ind * n_sites * 3 * 8 (3 GL, and 8 for the size of a double).

maybe,
cat my.gl | perl -an -e 'for($i=1; $i<=$#F; $i++){print(pack("d",$F[$i]))}' > my.glf
should be:
cat my.gl | perl -an -e 'for($i=0; $i<=$#F; $i++){print(pack("d",$F[$i]))}' > my.glf

[LZeitler]

That was it, thanks!