Error: Line 1 of .ped file has fewer tokens than expected.

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Shicheng Guo

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Mar 30, 2018, 2:32:45 PM3/30/18
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$   plink --file chr22 --make-bed --out chrY

I just download the VCF files from 1000 Genome:


This ped/map is coverted by: 

./vcftools --vcf input_data.vcf --plink --chr 1 --out output_in_plink


PLINK v1.90b5 64-bit (14 Nov 2017)             www.cog-genomics.org/plink/1.9/
(C) 2005-2017 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to chrY.log.
Options in effect:
  --file chr22
  --make-bed
  --out chrY

32112 MB RAM detected; reserving 16056 MB for main workspace.
Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.
Rescanning .ped file... 0%
Error: Line 1 of .ped file has fewer tokens than expected.


Interesting thing is chrMT, chrY is working well, but chr1, chr2 ... chr22, chrX is not working...

this is for chrY

 $ plink --file chrY --make-bed --out chrY
PLINK v1.90b5 64-bit (14 Nov 2017)             www.cog-genomics.org/plink/1.9/
(C) 2005-2017 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to chrY.log.
Options in effect:
  --file chrY
  --make-bed
  --out chrY

32112 MB RAM detected; reserving 16056 MB for main workspace.
Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (61995 variants, 1233 people).
--file: chrY-temporary.bed + chrY-temporary.bim + chrY-temporary.fam written.
61995 variants loaded from .bim file.
1233 people (0 males, 0 females, 1233 ambiguous) loaded from .fam.
Ambiguous sex IDs written to chrY.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 1233 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands
treat these as missing.
Total genotyping rate is -nan.
61995 variants and 1233 people pass filters and QC.
Note: No phenotypes present.
--make-bed to chrY.bed + chrY.bim + chrY.fam ... done.






Christopher Chang

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Mar 30, 2018, 2:37:14 PM3/30/18
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"plink --vcf" is more reliable than going through vcftools.
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