PLINK Haplotype blocks estimation not working

Question

[nsounac]

Hi,

I am using PLINK to estimate haplotype blocks using Gabriel's method. I am using the following command

plink --file Chr$PBS_ARRAY_INDEX --noweb --all --blocks --ld-window-kb 500

And it seemed to be working just fine but when job finished no blocks were called at all. The log file does not mention anything unusual (except for no block being called) and both plink.blocks file and plink.blocks.det are completely empty.

@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ plink.log ]
Analysis started: Fri Aug  5 16:27:21 2016

Options in effect:
    --file Chr10
    --noweb
    --all
    --blocks

Reading map (extended format) from [ Chr10.bim ] 
213835 markers to be included from [ Chr10.bim ]
Reading pedigree information from [ Chr10.fam ] 
480 individuals read from [ Chr10.fam ] 
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 480 missing
480 males, 0 females, and 0 of unspecified sex
Reading genotype bitfile from [ Chr10.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 213835 SNPs
480 founders and 0 non-founders found
Total genotyping rate in remaining individuals is 1
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 213835 SNPs
After filtering, 0 cases, 0 controls and 480 missing
After filtering, 480 males, 0 females, and 0 of unspecified sex
0 blocks called, writing list to [ plink.blocks ]
Writing extra block details to [ plink.blocks.det ]

Analysis finished: Sat Aug  6 01:57:29 2016

The error file I am getting from the computing server (PBS) is puzzling as well : all SNP are listed one by one but again no error whatsoever.

I tried running the haplotype estimation on a much smaller dataset (~ 3000 NP) and in an interactive run in PBS so I could see what was going on but still nothing wrong except that no blocks were called. Just out of curiosity, I used Haploview to estimate haplotype on that very same dataset (to see if the problem lied in my data) but Haploview could estimate haplotypes just fine.

Problem is that I have a fairly high number of SNP (~3 million) while not much time and Haploview is excruciatingly slow (~5 days for the smallest of my chromosomes)

Do you know what could be the problem ?

Thanks,

Nicolas

Answer 1

[awmackay]

I know this is an old post, but for anyone still interested...

We were just troubleshooting this problem as well and here is the issue: 0 individuals with nonmissing phenotypes

From the documentation: Note that only individuals with a non-missing phenotype are included in this analysis.

If you add a dummy phenotype, it works: sed -i 's/-9/12345/' my.ped

There is a "no phenotype" option in plink 1.9.

[Denis]

I've solved the issue by adding --blocks no-pheno-req to the plink 1.9 command line.

Answer 2

[alexmacharia]

thanks for the post , I was also got the error below.

Note: No phenotypes present. Warning: Skipping --blocks, since there are less than two founders with nonmissing phenotypes. (The 'no-pheno-req' modifier removes the phenotype restriction.)

included the command --blocks no-pheno-req and this sorted out the issue.