tabix errors when accessing 1000 Genomes data: "[E::bgzf_read] bgzf_read_block error -1 after 50219 of 52392 bytes" and Could not load .tbi/.csi index

Question

I am trying to access 1000 Genomes (1KG) data using tabix as per the 1KG tabix documentation "How do I get a genomic region sub-section of your files?" but am getting errors.

Command I'm running:

I am getting errors when I run the sample command provided in the docs:

tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz 2:39967768-39967768

Error message:

The error I'm getting is:

[E::bgzf_read] bgzf_read_block error -1 after 50219 of 52392 bytes
Could not load .tbi/.csi index of [...file name...]

Manual download

I tried to download a .tbi file and then run tabix as per this comment on GitHub but got an error

I ran:

wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/00-All.vcf.gz.tbi

which seemed to work, but this:

tabix ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/00-All.vcf.gz 1:17375-17375

returned an error:

hts_close returned non-zero status:

Other information

This worked for me a few days ago with the command above and my own queries, but I am now having issues.

I'm not very savvy with command line tools so it could very well be me, though the GUI Data Slicer tool for accessing 1KG files doesn't seem to be working right now, so perhaps it's a server-side thing.

Software

• I'm on a PC using the Windows Linux Subsystem
• I installed tabix via bioconda after having issues compiling it directly as specified in docs
• Since having this issue I have re-installed anaconda, bioconda, tabix, samtools, and htslib.

Tabix info

which tabix
/home/brouwern/anaconda3/bin/tabix

tabix --version

tabix (htslib) 1.3.1
Copyright (C) 2016 Genome Research Ltd.

Answer 1

try with https instead of ftp ?

$ tabix -h https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz 2:39967768-39967768  | cut -f1-8
##fileformat=VCFv4.0
##filedat=20101112
##datarelease=20100804
##samples=629
##description="Where BI calls are present, genotypes and alleles are from BI.  In there absence, UM genotypes are used.  If neither are available, no genotype information is present and the alleles are from the NCBI calls."
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GD,Number=1,Type=Float,Description="Genotype dosage.  Expected count of non-ref alleles [0,2]">
##FORMAT=<ID=OG,Number=1,Type=String,Description="Original Genotype input to Beagle">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=CB,Number=.,Type=String,Description="List of centres that called, UM (University of Michigan), BI (Broad Institute), BC (Boston College), NCBI">
##INFO=<ID=EUR_R2,Number=1,Type=Float,Description="R2 From Beagle based on European Samples">
##INFO=<ID=AFR_R2,Number=1,Type=Float,Description="R2 From Beagle based on AFRICAN Samples">
##INFO=<ID=ASN_R2,Number=1,Type=Float,Description="R2 From Beagle based on Asian Samples">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
2   39967768    rs11124691  T   A   .   PASS    DP=1991;AF=0.435;CB=UM,BI,BC,NCBI;EUR_R2=0.651;AFR_R2=0.742