I am trying to download NCBI databases through data manger using
Kraken2 Standard Database Builder database builder (Galaxy Version 2.0.7_beta)
An error occured while running the tool testtoolshed.g2.bx.psu.edu/repos/dfornika/data_manager_build_kraken2_database/kraken2_build_standard/2.0.7_beta.
Tool execution generated the following messages:
Fatal error: Exit code 1 ()
Possible unintended interpolation of @2 in string at /dep/_conda/envs/__kraken2@2.0.7_beta/bin/kraken2 line 16.
Possible unintended interpolation of @2 in string at /dep/_conda/envs/__kraken2@2.0.7_beta/bin/kraken2-build line 15.
Possible unintended interpolation of @2 in string at /dep/_conda/envs/__kraken2@2.0.7_beta/libexec/kraken2-build line 15.
Downloading nucleotide est accession to taxon map…rsync: link_stat “/taxonomy/accession2taxid/nucl_est.accession2taxid.gz” (in pub) failed: No such
file or directory (2)
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1650) [Receiver=3.1.2]
Traceback (most recent call last):
File “/data/shed_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data_manager_build_kraken2_database/65cbfb5e6f65/data_manager_build_kraken2_database/data_manager/kraken2_build_standard.py”,
line 113, in
main()
File “/data/shed_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data_manager_build_kraken2_database/65cbfb5e6f65/data_manager_build_kraken2_database/data_manager/kraken2_build_standard.py”,
line 106, in main
target_directory,
File “/data/shed_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data_manager_build_kraken2_database/65cbfb5e6f65/data_manager_build_kraken2_database/data_manager/kraken2_build_standard.py”,
line 47, in kraken2_build_standard
subprocess.check_call([‘kraken2-build’] + args, cwd=target_directory)
File “/usr/lib64/python2.7/subprocess.py”, line 542, 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’, ‘2019-04-24T222820Z_standard_kmer-len35_minimizer-len31_minimizer-spaces6’]’ returned non-zero exit status 23