Any fast way to download 1000 Genome Phase 3?
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4.5 years ago
b.ambrozio ▴ 30

Hello! I'm trying to download the 1000 Genomes (phase 3) through Aspera, but the instructions at the documentation don't work. Via command line (using ascp) I get the error: ERR [ascp] SSH authentication failed. Eg:

ascp -i /home/ibmuser/.aspera/connect/etc/asperaweb_id_dsa.putty -Tr -Q -l 100M -P33001 -L- fasp-g1k@fasp.1000genomes.ebi.ac.uk:vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi ./

Via Aspera Desktop I face: "SSH_MSG_DISCONNECT: 2 Too many authentication failures"

I have FTP in progress, but it's taking ages.

Thanks!

aspera fasp 1000genomes • 1.9k views
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I have tried the command on my computer and the file has been successfully downloaded, which version of ascp are you using? Is the private-key-file path correct?

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4.5 years ago
b.ambrozio ▴ 30

Ok, I got it working. The change was pretty much the -i parameter that in my case had to be for the new version of the ascp: asperaweb_id_dsa.putty. That's funny as yesterday I'm pretty sure I tried and didn't work (error "Too many authentication failures". I'm guessing the credential were blocked, or so...). Anyway, here's a script I've coded to download everything at once:

echo "Start: date"

FASP_ADDRESS="/home/ibmuser/.aspera/connect/etc/asperaweb_id_dsa.openssh -Tr -Q -l 100M -P33001 -L- fasp-g1k@fasp.1000genomes.ebi.ac.uk:vol1/ftp/release/20130502"

for CHR in $(seq 1 22); do
FILE=ALL.chr$CHR.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz echo "Downloading '$FILE'..." echo "ascp -i $FASP_ADDRESS/$FILE ./" done

echo "End: date"

It's available for download from my Github too (with along an FTP version, if you will): https://github.com/bambrozio/bioinformatics/tree/master/utils

Thanks!

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The downloads from https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 are ~70% smaller, and contain all the information in the VCFs (“plink2 —pfile ... —export vcf bgz” can be used to generate actual VCFs).

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