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mfumagalli / ngsPopGen

Population genetics analyses from NGS data
GNU General Public License v3.0
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ngsStat Floating point exception (core dumped) #9

Closed madzafv closed 3 years ago

madzafv commented 5 years ago

Hello, I'm trying to use ngsStat by doing: ./ngsStat -npop 1 -postfiles file.saf -nind 11 -outfile file.stat where my .saf (out of angsd) looks like:

NC_007897.1     2       0.000000        -5.094189       -10.313600      -15.673835      -21.194906      -26.905237      -32.847622      -39.091530      -45.764591      -53.156807      -62.342842      -73.078079      -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf
NC_007897.1     3       0.000000        -5.217402       -10.582065      -16.106823      -21.804443      -27.695183      -33.814251      -40.223988      -47.043053      -54.543686      -63.845039      -75.157547      -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf
NC_007897.1     4       0.000000        -5.217465       -10.582220      -16.107111      -21.804922      -27.695948      -33.815476      -40.226013      -47.046764      -54.552528      -63.910259      -75.850700      -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf
NC_007897.1     5       0.000000        -5.217465       -10.582220      -16.107111      -21.804922      -27.695948      -33.815476      -40.226013      -47.046764      -54.552528      -63.910259      -75.850700      -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf    -inf

but I'm getting the error:

Floating point exception (core dumped)

Any ideas what could be wrong?

mfumagalli commented 5 years ago

Hi Madza! I think you missed the -nsites option. But more importantly, why are you using ngsStat? Most of these statistics are much better implemented in ANGSD so I encourage you to use ANGSD instead of ngsStat.

madzafv commented 5 years ago

Hummm I get another error when I use the -nsites -> Possible error reading SFS, binary file might be broken... Yeah, I'm using angsd for most stuff, but it doesn't calc het in a window does it? Or fixed sites between 2pops? Guess I have to write something to do it... thxs!

mfumagalli commented 5 years ago

Usually you get that error when the -nind option is in conflict with the actual dimensions of .saf files. Did you fold the data? ngsTools doesn't really support folded data. Let me know.

mfumagalli commented 3 years ago

closed since no further requests for made