Failed Create Kraken2 database after a long time downloading.

1

hi, I’m trying to create a Kraken2 standard database through “Kraken2 database builder” (version: 2.1.1 by iuc), but after download all the database, it occurs an error:

error
An error occurred with this dataset:
Downloading nucleotide gb accession to taxon map... done.
Downloading nucleotide wgs accession to taxon map... done.
Downloaded accession to taxon map(s)
Downloading taxonomy tree data... done.
Uncompressing taxonomy data... done.
Untarring taxonomy tree

when I click the debug info:
…
Downloading plasmid files from FTP…Traceback (most recent call last):
File “/cygene/work/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/dfornika/data_manager_build_kraken2_database/ffeb852407d6/data_manager_build_kraken2_database/data_manager/kraken2_build_database.py”, line 361, in
main()
File “/cygene/work/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/dfornika/data_manager_build_kraken2_database/ffeb852407d6/data_manager_build_kraken2_database/data_manager/kraken2_build_database.py”, line 317, in main
data_manager_output = kraken2_build_standard(
File “/cygene/work/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/dfornika/data_manager_build_kraken2_database/ffeb852407d6/data_manager_build_kraken2_database/data_manager/kraken2_build_database.py”, line 84, in kraken2_build_standard
subprocess.check_call([‘kraken2-build’] + args, cwd=target_directory)
File “/usr/lib/python3.8/subprocess.py”, line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ‘[‘kraken2-build’, ‘–threads’, ‘1’, ‘–standard’, ‘–kmer-len’, ‘35’, ‘–minimizer-len’, ‘31’, ‘–minimizer-spaces’, ‘6’, ‘–db’, ‘2021-04-19T012759Z_standard_kmer-len_35_minimizer-len_31_minimizer-spaces_6’]’ returned non-zero exit status 123.

please help!

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1 Like
2

Hi @levinyi

There are updated wrapped versions of the Kraken2 tool suite, including a Data Manager. Try the most current versions owned (authored) by the IUC. Install/update Kraken2 first, then the matching updated Data Manager, then run the Data Manager. It would probably best to uninstall any outdated tool versions and to remove partial data installs that you will be replacing first, to avoid confusion/mixups, or (importantly) conflicts between different base tool wrappers.

If you are not upgraded to the most current version of Galaxy, also do that, as it tends to resolve many administrative issues:

*Releases — Galaxy Project 21.01 documentation
*https://toolshed.g2.bx.psu.edu/ – Search with the keyword “kraken” to find all tools. The last revision date and author will be listed.
*https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/0eebe086fd58 – most current Data Manager
*http://datacache.galaxyproject.org/ – pre-built indexes are also availabe and can be installed from this source as an alternative