Cannot update accessions: failed download

[vfonti]

When I run updateAccessions.sh (both locally and on an HPC server) i get this error message: "Update failed. Is your internet connection okay?".
I tried to download accession files to add them manually but the download failes, even trying with different browsers. Can anybody help with this?

Regs.

[ReneKat]

Hi @vfonti
I was having the same error message.
I was able to download all the files manually by right-clicking on the hyperlink, saving the link location, and running wget in my command line.

mkdir KronaTools/taxonomy
cd KronaTools/taxonomy
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/dead_prot.accession2taxid.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/dead_wgs.accession2taxid.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/nucl_wgs.accession2taxid.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz

cd KronaTools/
./updateTaxonomy.sh
./updateAccessions.sh

Hope that helps!

Best,
René

[vfonti]

Hi @ReneKat,
Thanks for replying. Unfortunately, I've tried to download them manually with no success. Tried also your codes but I keep having the same problem.
Maybe those file have changed location?

[Koen-vdl]

Hi @vfonti
I was having the same error message.
I was able to download all the files manually by right-clicking on the hyperlink, saving the link location, and running wget in my command line.

mkdir KronaTools/taxonomy
cd KronaTools/taxonomy
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/dead_prot.accession2taxid.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/dead_wgs.accession2taxid.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/nucl_wgs.accession2taxid.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz

cd KronaTools/
./updateTaxonomy.sh
./updateAccessions.sh

Hope that helps!

Best,
René

I think what misses here is the manual downloads need to be migrated to the taxonomy db location
Additionally you need to specify the files don't need to be downloaded again by adding --only-build to

./updateTaxonomy.sh --only-build
./updateAccessions.sh --only-build

[quliping]

Hi @ReneKat, Thanks for replying. Unfortunately, I've tried to download them manually with no success. Tried also your codes but I keep having the same problem. Maybe those file have changed location?

1. I don't know the reason but the 'ftp.ncbi.nih.gov' is not available for any downloading commonds of our server (linux system), you should use 'ftp.ncbi.nlm.nih.gov'.
2. The location of 'taxdump.tar.gz' file and 'accession2taxid.gz' files should be '/taxonomy' and '/taxonomy/accession2taxid', respectively. Therefore, you should make a folder named 'accession2taxid' under '~/taxonomy/' then put 'accession2taxid.gz' files in 'accession2taxid'.

After all, you should run:
./updateTaxonomy.sh --only-build
./updateAccessions.sh --only-build