These are chat archives for theboocock/selectionTools

5th
May 2015
murraycadzow
@murraycadzow
May 05 2015 01:37

Hi,
I have had this problem in my own data and did change the way multicore_iHH.R rejoined the individual iHH files after the calculation step.
The new method was updated into the selectionTools1.1 branch. It requires running the also updated haps_interpolate step before the updated multicore_iHH.R
Changing window size is valid, ideally a larger window size is used where possible so that the ehh decay for the SNPs isn't prematurely stopped at the window boundary

Murray

Paloma Contreras
@PalomaUChile
May 05 2015 19:56
I'm using the updated scripts now, and multicore_iHH.R doesn't work, not even with the chromosomes that were OK before.
When I run this:
Rscript /sfw/selectionTools/selectionTools/corescripts/multicore_iHH.R -p AYM -i AYM_genetic_dist.haps -c 16 --window 5000000 --overlap 2000000 --maf 0.0 --big_gap 200000 --small_gap 20000 --small_gap_penalty 20000 --haplo_hh --physical_map_haps AYM_genetic_dist.pos --cores 40 --working_dir . --offset 1 --ihs
Paloma Contreras
@PalomaUChile
May 05 2015 20:07
the error message is:
Error in [.data.frame(map_positions, , 2) : undefined columns selected
Calls: [ -> [.data.frame
Execution halted
(because the file AYM_genetic_dist.pos has 1 column even if I use the new script haps_interpolate to build it)
Paloma Contreras
@PalomaUChile
May 05 2015 20:20
I changed the Rscript so it can use the first column in the .pos file, and finally, I got the same problem as before:
[1] "t_AYM.haps13.iHH does not exist! Continuing without"
[1] "t_AYM.haps14.iHH does not exist! Continuing without"
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32
Error in [<-.data.frame(*tmp*, , 3, value = 16) :
new columns would leave holes after existing columns
Calls: [<- -> [<-.data.frame
Execution halted
Paloma Contreras
@PalomaUChile
May 05 2015 20:32
What can I do?