These are chat archives for theboocock/selectionTools

May 2015
Paloma Contreras
May 04 2015 13:41

Thanks for your answer! Sorry to bother you again, but now I'm having a problem running the pipeline.
This time I'm using my own dataset and it worked well, except for three chromosomes (1, 9 and 16) that didn't complete the analysis correctly.
The command that fails is:

multcore_ihh command = Rscript /sfw/selectionTools/selectionTools/corescripts/multicore_iHH.R -p AYM -i AYM_genetic_dist.haps -c 9 --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

once I run it, it returns this message:

Error in [<*tmp*, , 2, value = c(45440, 109810, 175050, :
replacement has 14060 rows, data has 13391
Calls: [<- -> [<

I have checked the .haps and .pos file and they have the same amount of SNPs. Could it be a problem with some gaps in my dataset? I thought that the pipeline should just skip those regions (with gaps) and continue computing the iHS.

I tried changing the window's size to 8Mb and it worked, but I'm not sure if that's the right way to solve it or if there is any better way to do it.
I would really appreciate you advice in this matter. Thanks a lot!