I am trying to convert vcf format to plink format. I use this dataset (ALL.2of4intersection.20100804.genotypes.vcf.gz). Following is the command I used in my cmd:
plink2 --vcf ALL.2of4intersection.20100804.genotypes.vcf.gz --make-bed --out ALL.2of4intersection.20100804.genotypes
However, I have an error as follows: Error: --vcf file decompression faliure: Malformed BGZF block
Then, I tried to unzip the gz file as follows to check whether I can unzip it: gzip -d ALL.2of4intersection.20100804.genotypes.vcf.gz
Again, there is an error as follows: gzip: ALL.2of4intersection.20100804.genotypes.vcf.gz: invalid compressed data--crc error gzip: ALL.2of4intersection.20100804.genotypes.vcf.gz: invalid compressed data--length error
It would be very helpful if you could give me your suggestion for this error messages. Thank you!
I am trying to use following command to downlaod the file with population information of 1000 genomes.
But I have an error as follows:
--2022-09-29 11:06:10-- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/20100804.ALL.panel => ‘20100804.ALL.panel’ Resolving ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)... failed: Temporary failure in name resolution. wget: unable to resolve host address ‘ftp.1000genomes.ebi.ac.uk’
Could you pls help me to check whether I used corret code to download this file? Thank you!
If you continue getting the following error
then ot is a local problem on your end. DNS is not able to resolve the name correctly. Wait and see if the problem resolves.
Thank you for your information. I just tried with your command and got the error as Temporary failure in name resolution. Did you mean like "wait and see if the problem resolves", means, do I need to re -reun after waiting some time please? kindly let me know. Thank you!
Correct. This looks like a problem with your local network. I was able to access the link without problems.
Thank you so much! I just check my workinf directory with "ls" and I was able to find the file name "20100804.All.panel". Does this means it was downloaded successfully? Pls let me know how can I make sure it? Thank you!
As long as the file is not empty it should be good.
Thank you so much! Will try to run the analysis with the file and check it! Thanks again!!