Score:1

SRA Toolkit Error while using prefetch

cn flag

I installed the SRA toolkit using these commands:

cd ~/Downloads

wget http://old-releases.ubuntu.com/ubuntu/pool/universe/n/ncbi-vdb/libncbi-vdb2_2.9.3+dfsg-2_amd64.deb 
wget http://old-releases.ubuntu.com/ubuntu/pool/universe/n/ncbi-vdb/libncbi-wvdb2_2.9.3+dfsg-2_amd64.deb 
wget http://old-releases.ubuntu.com/ubuntu/pool/universe/s/sra-sdk/sra-toolkit_2.9.3+dfsg-1build2_amd64.deb

sudo apt-get install ./libncbi-vdb2_2.9.3+dfsg-2_amd64.deb 
sudo apt-get install ./libncbi-wvdb2_2.9.3+dfsg-2_amd64.deb

cat <<EOF | sudo tee /etc/apt/preferences.d/pin-sra-libs 
Package: libncbi-vdb2 
Pin: version 2.9.3+dfsg-2 
Pin-Priority: 1337

Package: libncbi-wvdb2 
Pin: version 2.9.3+dfsg-2 
Pin-Priority: 1337 
EOF

sudo apt-get install ./sra-toolkit_2.9.3+dfsg-1build2_amd64.deb

After installation I downloaded an SRA file and when I tried to download another SRA file then it gave me following error:

prefetch:` symbol lookup error: /lib/x86_64-linux-gnu/libncbi-vdb.so.2: undefined symbol: vdb_mbedtls_md_setup

How can I solve this?

Score:0
zw flag

It looks like you are following my answer. It was written 1.5 year ago. Something may change.

According to https://github.com/ncbi/sra-tools/issues/546 you have to remove this locally installed version of SRA by

sudo rm /etc/apt/preferences.d/pin-sra-libs
sudo apt-get purge --autoremove libncbi-vdb2 libncbi-wvdb2 sra-toolkit

and install newest version from https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software instead.

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