Mismatch between number of lines in plink .ped files and corresponding .map file

[AnnaRu]

I have a problem with a mismatch between the number of columns in a plink .ped file and the corresponding map file; when I try to produce a .bed file I get the error message below.

I would be really really grateful for any input on this!

17028030 (of 17028030) markers to be included from [ raw_phased.map ]

ERROR:
A problem with line 1 in [ raw_phased.ped ]
Expecting 6 + 2 * 17028030 = 34056066 columns, but found 20352684

The ped.file has the first 6 columns and they seem correct. The map file seems fine too. Code used below:


I have used an unfiltered vcf file to make sure that it is not due to filtering issues, and phased it using beagle:


module load beagle

java -Xmx4000m -jar /projects/cees/bin/beagle-4.0/b4.r1274.jar gt=../islands_parents_treeHM60_1.vcf ibd=true out=raw_phased nthreads=16 phase-its=10


Then I use vcftools to produce the plink .ped and map files

vcftools --gzvcf raw_phased.vcf.gz --plink --out raw_phased

Then the problem arises when I try to produce .bed and .raw files using plink
(version 1.07, the only one on the cluster, so that is how it has to be). In these steps no files are produced and the error message on top is displayed in the plink.log

#making bed file with plink
plink --file raw_phased --make-bed

#produce a .raw file that can be read into R using read.table
plink --recodeA --file raw_phased