Question: R, PopGenome Package. Cannot open file
0
gravatar for pifferdavide
4.8 years ago by
pifferdavide100
Italy
pifferdavide100 wrote:

I downloaded the Chromosome in vcf format along with the tbi file from 1000 Genomes ftp server. I installed the packaged "PopGenome". However, I cannot open the files. I type this command and get an error message. Am I missing something? 

readVCF("C:/Users/Davide/Documents/chr22/Chr22.vcf", 1000,"22",1,100000)
open: No such file or directory
Caught exception inside whop_tabix::open('C:/Users/Davide/Documents/chr22/Chr22.vcf.gz"):
    'whop_tabix::open : Failed to open tabix index file'
return FALSE from whoptabix_open
vcff::open : could not open tabix-index!
VCF_open : Could not open file 'C:/Users/Davide/Documents/chr22/Chr22.vcf' as tabix-indexed!
[1] FALSE

 

snp popgenome R • 2.8k views
ADD COMMENTlink modified 4.6 years ago by bastianxpfeifer50 • written 4.8 years ago by pifferdavide100

I have both files in the same folder and I downloaded from here: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

ADD REPLYlink written 4.8 years ago by pifferdavide100

Did you try this: GENOME.class=readVCF() instead of just readVCF()?

By the way, the example .VCF file didn't have a tabix-index file with it, why it can load in successfully?

 

ADD REPLYlink written 4.7 years ago by huan192010

Hi ALL, see also http://popgenome.weebly.com/

THX, all the best.

Bastian

ADD REPLYlink modified 4 weeks ago by RamRS24k • written 4.6 years ago by bastianxpfeifer50
0
gravatar for RamRS
4.8 years ago by
RamRS24k
Houston, TX
RamRS24k wrote:

You should have a Chr22.vcf.tbi tabix index in the same folder as the VCF file. If that doesn't exist, you can always create one as shown here: http://samtools.sourceforge.net/tabix.shtml

ADD COMMENTlink modified 4 weeks ago • written 4.8 years ago by RamRS24k

I do have a Chr22.vcf.tbi tabix index in the same folder.

ADD REPLYlink written 4.8 years ago by pifferdavide100

Can you check the permissions on the file please? Also Windows might set security flags on downloaded files that you might have to "unblock".

ADD REPLYlink written 4.8 years ago by RamRS24k

You were indeed right but it's still not working, even after I unblocked both files...still getting same error message!

ADD REPLYlink written 4.8 years ago by pifferdavide100

Can you try, on R:

Sys.chmod("C:/Users/Davide/Documents/chr22/Chr22.vcf", mode = "0777",showWarnings=TRUE)
Sys.chmod("C:/Users/Davide/Documents/chr22/Chr22.vcf.tbi", mode = "0777",showWarnings=TRUE)
ADD REPLYlink modified 4 weeks ago • written 4.8 years ago by RamRS24k

I tired it but I get no output

ADD REPLYlink written 4.8 years ago by pifferdavide100
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