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fbreitwieser / krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
GNU General Public License v3.0
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Trouble downloading viral neighbors database #165

Open jalalsiddiqui opened 6 months ago

jalalsiddiqui commented 6 months ago

I tried to download the "viral neighbors" database (as well as RefSeq) using the code below.

krakenuniq-download --db DBDIR refseq/viral/Any viral-neighbors

Unfortunately, we run into the following error below:

Downloading assembly summary file for viral genomes, and filtering to assembly level Any. Downloading viral genomes: 14992/14992 ... Found 14992 files. Downloading viral neighbors. Downloading DBDIR/taxonomy/nucl_gb.accession2taxid.gz [curl -g 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz' -o 'DBDIR/taxonomy/nucl_gb.accession2taxid.gz'] ... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 2283M 100 2283M 0 0 43.4M 0 0:00:52 0:00:52 --:--:-- 63.1M done (53s) DBDIR/taxonomy/nucl_gb.accession2taxid.gz check [2.23 GB] SUCCESS Sorting maping file (will take some time) [gunzip -c DBDIR/taxonomy/nucl_gb.accession2taxid.gz | cut -f 1,3 > DBDIR/taxonomy/nucl_gb.accession2taxid.sorted.tmp && sort --parallel 5 -T DBDIR/taxonomy DBDIR/taxonomy/nucl_gb.accession2taxid.sorted.tmp > DBDIR/taxonomy/nucl_gb.accession2taxid.sorted && rm DBDIR/taxonomy/nucl_gb.accession2taxid.sorted.tmp] ... done (4m22s) DBDIR/taxonomy/nucl_gb.accession2taxid.sorted check [4.77 GB] Reading names file ... Downloading DBDIR/taxonomy/taxdump.tar.gz [curl -g 'https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' -o 'DBDIR/taxonomy/taxdump.tar.gz'] ... Download taxdump.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0curl: (6) Could not resolve host: ftp.ncbi.nih.gov 1536 at /***/tools/miniconda3/envs/krakenuniq/bin/krakenuniq-download line 775.

It seems that it cannot resolve the host. We are sure what is going on and will appreciate any help you can provide.

Thanks a bunch!

jpod1010 commented 6 months ago

I ran into this problem as well - the solution for now is to download the taxdump and untar it manually

curl -g https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz -o $Your_DB/taxonomy/taxdump.tar.gz tar -xvf $Your_DB/taxonomy/taxdump.tar.gz

jalalsiddiqui commented 6 months ago

Thanks a bunch! Tried it and it worked!