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Connecting to Web... problem in plink?

I need to convert a bed file into vcf and decided to use plink. But whenver I wrote command plink (it happens both with parameters and when I just write "plink"), it gives the following error

@----------------------------------------------------------@
|        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/        |
@----------------------------------------------------------@

Web-based version check ( --noweb to skip )
Connecting to web...  failed connection

Problem connecting to web

Writing this text to log file [ plink.log ]
Analysis started: Fri Aug 11 15:07:16 2023

Options in effect:

Before frequency and genotyping pruning, there are 0 SNPs
0 founders and 0 non-founders found
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 0 SNPs

ERROR: Stopping as there are no SNPs left for analysis

How to resolve this issue or are there any better way of converting bed to vcf. (Im connected to a remote server and have no right to change the environment.)

plink bed vcf
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written by guntul • guntul

The problem does not appear to be the web connection. You can remove that warning by adding --noweb to your command line.

Provide the command you are trying to run.

• 0 views • link
written by GenoMax GenoMax

1 answer

Why don't you use PLINK 1.9 or PLINK 2.0 which are way faster than PLINK 1.07 unless you have any specific reason to use the older version? These two latest versions can directly convert your bed/bim/fam files into vcf.

plink --bfile [Your filename prefix] --recode vcf --out [Output VCF prefix]
• 0 views • link
written by bk11 • bk11

It is the one in the server, I dont have permission to update

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written by guntul • guntul

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