plink 1.9: Warning: No output requested. Exiting. - works with 1.07

[Sanjeev Sariya]

Hello there,

I'm new to plink and GWAS analysis.

I'd like to get basic case-control, male-female details from my files using v1.9. Folder where I'm running plink has .bim, .bam, .bed file. I started my tutorial with plink 1.07 where upon running following command I get basic information:

plink --bfile w_newqc 

However, with plink1.09 I get error: "Warning: No output requested.  Exiting."

Even if I try:  plink1.9 --bfile w_newqc --out Frew_newqc 

I get same error. How can I replicate information which I get using plink 1.07

Kindly help.

[Christopher Chang]

This works if you add any command; a simple one like --write-snplist will do.

[Sanjeev Sariya]

Hi Chris,

Thanks for your reply. Mentioned command works and helps me extract SNP list in v1.9. 

However, I'm interested to get information such as below  (obtained from v1.07) from newer version of plink:

Before frequency and genotyping pruning, there are 236071 SNPs

914 founders and 0 non-founders found

156 heterozygous haploid genotypes; set to missing

Writing list of heterozygous haploid genotypes to [ plink.hh ]

Total genotyping rate in remaining individuals is 0.998625

0 SNPs failed missingness test ( GENO > 1 )

0 SNPs failed frequency test ( MAF < 0 )

After frequency and genotyping pruning, there are 236071 SNPs

After filtering, 554 cases, 360 controls and 0 missing

After filtering, 369 males, 545 females, and 0 of unspecified sex

How do I get basic information about pruning using v1.9? 

Apologies for inconvenience.

Thanks,

Sanjeev

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[Christopher Chang]

It should have been printed as part of the --write-snplist .log output?

[Sanjeev Sariya]

Thanks.