ERROR: Parsing line 0 : incorrect number of columns, observed: 1 expected: 3

[jessicahr]

I'm trying to run Shapeit4 with some files and I obtain en Error (ERROR: Parsing line 0 : incorrect number of columns, observed: 4 expected: 3). I even tried with the unphased file in /test and I have the same error.

This is how I used it (same with .vcf): shapeit4 --input unphased.bcf --map ../maps/genetic_maps.b37.tar.gz --region 20 --output test-phased.bcf

This is the log, I don't obtain an output file: << SHAPEIT

• Author : Olivier DELANEAU, University of Lausanne
• Contact : olivier.delaneau@gmail.com
• Version : 4.1.2
• Run date : 11/03/2021 - 13:25:50

Files:

• Input VCF : [unphased.bcf]
• Genetic Map : [../maps/genetic_maps.b37.tar.gz]
• Output VCF : [test-phased.bcf]

Parameters:

• Seed : 15052011
• Threads : 1 threads
• MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
• PBWT : Depth of PBWT neighbours to condition on: 4
• PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM]
• HMM : K is variable / min W is 2.50cM / Ne is 15000
• HMM : Recombination rates given by genetic map
• HMM : !AVX2 optimization inactive!
• IBD2 : length>=3.00cM [N>=150 / MAF>=0.010 / MDR<=0.500]

Initialization:

• VCF/BCF scanning [N=203 / L=24990 / Reg=20] (0.01s)
• VCF/BCF parsing [Hom=90.0% / Het=10.0% / Mis=0.0%] (0.08s)

ERROR: Parsing line 0 : incorrect number of columns, observed: 4 expected: 3

Does anyone had the same problem?? Thank you so much!

[odelaneau]

Untar genetic_maps.b37.tar.gz first and then specify the file matching your chr with --map.

Cheers,

[jessicahr]

That was the problem! Thank you so much! You can delete this Issue because it's just that I was not using the correct map.

Thanks!