Plink Error

Question

[Amokelani]

Hi I am trying to convert ped file for hapmap3 I downloaded here https://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2009-01_phaseIII/plink_format/ and unzipped with binzip2 but I am getting the following error when running this command

PLINK v1.90b5.2 64-bit (9 Jan 2018)            www.cog-genomics.org/plink/1.9/
(C) 2005-2018 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to /cbio/projects/003/Amokelani/MPV17_pacbio/Shapeit2/HapMapIII_NCBI36.log.
Options in effect:
  --make-bed
  --out HapMapIII_NCBI36
  --ped hapmap3_r2_b36_fwd.consensus.qc.poly

241814 MB RAM detected; reserving 120907 MB for main workspace.
Error: Failed to open .

I am not sure what it means or how to fix it. This is my command

/cbio/projects/003/soft/plinkv1.90b5.2/plink --ped hapmap3_r2_b36_fwd.consensus.qc.poly --make-bed --out 

I'm pretty sure I spelled the filename correctly

Answer 1

[bk11]

You should be able to create bed/bim/fam files, please do followings-

#Unzip ped/map files first
bunzip2 hapmap3_r2_b36_fwd.consensus.qc.poly.ped.bz2
bunzip2 hapmap3_r2_b36_fwd.consensus.qc.poly.map.bz2

#Use plink to convert ped/map into bed/bim/fam files
plink --file hapmap3_r2_b36_fwd.consensus.qc.poly --make-bed --out hapmap3_r2_b36_fwd.consensus.qc.poly

Answer 2

[chrchang523]

My mistake with that error message; it should instead tell you that you did not specify a .map file.

You probably mean —file where you used —ped.