Can't run updateTaxonomy.sh and updateAccessions.sh even use the latest version 2.7.1

[lulunisrna]

Dear Everyone,

I installed krona trough conda and get krona version 2.7.1 When I run updateTaxonomy.sh with command ./updateTaxonomy.sh I get error like this:

Fetching taxdump.tar.gz (if newer than taxonomy.tab)... Failed to set filetime 1582413967 on outfile: No such file or directory

Cleaning up...

Finished.

When I try to open taxdump.tar.gz it's cannot reach in to the ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz And when I run ./updateAccession i get erros like this:

Fetching accession2taxid/nucl_gb.accession2taxid.gz...

Update failed. Is your internet connection okay?

How to solve this problem? I already used the last version of Krona 2.7.1 Thank you for your help

Regards, Lulu

[Koen-vdl]

had the same issue: used this workaround

#create krona_env with krona
conda create -n krona_env krona  -y
conda activate krona_env

# delete a symbolic link that is not correct
rm -rf ~/miniconda3/envs/krona_env/opt/krona/taxonomy

#  create a directory in  home where the krona database will live
mkdir -p ~/krona/taxonomy

# now we make a symbolic link to that directory
ln -s ~/krona/taxonomy ~/miniconda3/envs/krona_env/opt/krona/taxonomy

# the krona downloader fails when downloading the latest NCBI db
# ktUpdateTaxonomy.sh ~/krona/taxonomy
# taxdump.tar.gz needs to be downloaded manually from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 
# taxdump.tar.gz needs to be placed in ~/krona/taxonomy
# then one needs to run  ktUpdateTaxonomy.sh --only-build
ktUpdateTaxonomy.sh --only-build

[rebeelouise]

had the same issue: used this workaround

#create krona_env with krona
conda create -n krona_env krona  -y
conda activate krona_env

# delete a symbolic link that is not correct
rm -rf ~/miniconda3/envs/krona_env/opt/krona/taxonomy

#  create a directory in  home where the krona database will live
mkdir -p ~/krona/taxonomy

# now we make a symbolic link to that directory
ln -s ~/krona/taxonomy ~/miniconda3/envs/krona_env/opt/krona/taxonomy

# the krona downloader fails when downloading the latest NCBI db
# ktUpdateTaxonomy.sh ~/krona/taxonomy
# taxdump.tar.gz needs to be downloaded manually from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 
# taxdump.tar.gz needs to be placed in ~/krona/taxonomy
# then one needs to run  ktUpdateTaxonomy.sh --only-build
ktUpdateTaxonomy.sh --only-build

This worked perfectly - thanks!

[tantascamila]

Hi!

I had to replace miniconda for anaconda3 and then it worked. I had to extract the files from the taxdump.tar.gz as well.

Hope these tips help newies like me...

#create krona_env with krona conda create -n krona_env krona -y conda activate krona_env

delete a symbolic link that is not correct

rm -rf ~/anaconda3/envs/krona_env/opt/krona/taxonomy

create a directory in home where the krona database will live

mkdir -p ~/krona/taxonomy

now we make a symbolic link to that directory

ln -s ~/krona/taxonomy ~/anaconda3/envs/krona_env/opt/krona/taxonomy

the krona downloader fails when downloading the latest NCBI db

ktUpdateTaxonomy.sh ~/krona/taxonomy

taxdump.tar.gz needs to be downloaded manually from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

taxdump.tar.gz needs to be placed in ~/krona/taxonomy

then one needs to run ktUpdateTaxonomy.sh --only-build

ktUpdateTaxonomy.sh --only-build

[Mayurk619]

I followed all the steps above, I did md5sum to check if I manually downloaded is correct, however, I'm getting this error:

Update failed. Could not find taxonomy source files in ~/anaconda3/envs/krona_env/opt/krona/taxonomy.

When I run ktUpdateTaxonomy.sh ~/krona/taxonomy. Fetching and checking md5sum was finished. When I run ktUpdateTaxonomy.sh --only-build I get the above error.

[rturba]

I have the same issue as @Mayurk619 as well, but in my case is with updateAccession.sh --only-build. I have installed krona through conda:

conda install -n kraken2 -c bioconda krona

I'm able to run the ktUpdateTaxonomy.sh --only-build with no problems, though.