Hello. I am trying to extract data from .bed file using the following command:
~/data/df$ plink --bed Obesity_Send.bed --bim Obesity_Send.bim --fam Obesity_Send.fam --keep-fam ii.txt --make-bed --out ii
Here is the plink log from problematic run.
PLINK v1.90b6.25 64-bit (5 Mar 2022) Options in effect: --bed Obesity_Send.bed --bim Obesity_Send.bim --fam Obesity_Send.fam --keep-fam ii.txt --make-bed --out ii
Hostname: cohort-700-l-0 Working directory: /home/jovyan/data/df Start time: Thu Mar 31 11:12:41 2022
Random number seed: 1648725161 30153 MB RAM detected; reserving 15076 MB for main workspace.
2655566 variants loaded from .bim file.
522 people (123 males, 399 females) loaded from .fam.
291 phenotype values loaded from .fam.
Error: Failed to open ii.txt.
End time: Thu Mar 31 11:12:42 2022
please help, since I'm new to plink
Failed to open ii.txtprobably meansii.txtisn't the current directory.got it, i created ii.txt file and run the command then this error throwing:
log :
PLINK v1.90b6.25 64-bit (5 Mar 2022) Options in effect: --bed Obesity_Send.bed --bim Obesity_Send.bim --fam Obesity_Send.fam --keep-fam ii.txt --make-bed --out ii
Hostname: cohort-700-l-0 Working directory: /home/jovyan/data/df Start time: Thu Mar 31 11:53:41 2022
Random number seed: 1648727621 30153 MB RAM detected; reserving 15076 MB for main workspace.
2655566 variants loaded from .bim file.
522 people (123 males, 399 females) loaded from .fam.
291 phenotype values loaded from .fam.
Error: No people remaining after --keep-fam.
End time: Thu Mar 31 11:53:41 2022
Actually i need to extract sample id's, how to do so?