Error when importing dosage file using PLINK2 for imputation analysis

Question

[hkj7]

Hi all, I have a file of imputed dosage genotypes with the header (contains the Individual and family ID) and looks like this:

9:10163:CT:C 10163 CT C 0 0 0 0 0 0 0 0 0 0.001 0.001 0 0 0 0 0.01 0 0 0 0 0 0 0 0.005 0 0 0.001 0 0 0 0 0 0 0 0 0 0 0 0 0.034 0 0 0 0 0 0.001 0 0 0 0 0.001 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.004 0 0.103 0 0 0 0 0 0.002 0 0 0 0 0 0 0 0 0 0 0 0 0 0.005 0 0 0 0 0 0 0 0 0 0 0 0 0 0.007 0 0 0.002 0 0 0 0 0 0 0 0 0 0 0 0.003

I have one fam file containing the IDs, maternal and paternal which is 0 and the last column contains the phenotype data for one phenotype. The fam file looks like this:

1 RQ14004-3 0 0 1 8.366666667
2 RQ14028-1 0 0 1 11.90333333 
3 RQ14034-5 0 0 1 4.97 
4 RQ14001-5 0 0 1 22.5 
5 RQ14002-7 0 0 2 47.13666667

The map file looks like this (I have map files for each chromosome):

1 1:10177:A:AC 0 10177
1 rs145072688:10352:T:TA 0 10352
1 rs376342519:10616:CCGCCGTTGCAAAGGCGCGCCG:C 0 10616
1 1:10642:G:A 0 10642
1 1:11008:C:G 0 11008
1 1:11012:C:G 0 11012
1 1:13110:G:A 0 13110
1 rs201725126:13116:T:G 0 13116
1 rs200579949:13118:A:G 0 13118
1 1:13273:G:C 0 13273

I am running this script but it doesn't run. I get no output. My PLINK version 2 works okay, but I am not sure why I get no output. I have headers for each of the dosage files? Would this cause a problem? I am also using separate dosage files for each chromosome rather than a merged dosage file with all the chromosomes together. Which is why I have the #PBS -t 1-23 in the header of my plink script. This is the plink command I use:

    #!/bin/bash
    #PBS -N dosageformat_test
    #PBS -l walltime=06:00:00
    #PBS -l pvmem=4gb
    #PBS -t 1-23

i=$PBS_ARRAYID

cd /rfs/REQUITE/Shared/RILA/genotypes/dosage_files

file="PLINK_requite_ids.dose.oncoarray_requite_chr${i}_unphased_filtered_rila.txt.gz"
map="chr${i}.map"
out="chr${i}init"

exec plink2 --threads 1 --import-dosage ${file}  skip0=1 skip1=1 format=1 --fam RILA.fam --map ${map} --out ${out}

Any help would be so beneficial. Thank you!

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.