Question: error downloading databases
0
gravatar for lotta.purkamo
6 months ago by
lotta.purkamo0 wrote:

I'm trying to download databases via admin by running data manager tools and I get an error message: Fatal error: Exit code 1 (Error) /bin/sh: humann2_databases: command not found Traceback (most recent call last): File "/Users/lplotta/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann2_database_downloader/9244804f69a7/data_manager_humann2_database_downloader/data_manager/data_manager_humann2_download.py", line 170, in <module> target_dir) File "/Users/lplotta/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann2_database_downloader/9244804f69a7/data_manager_humann2_database_downloader/data_manager/data_manager_humann2_download.py", line 119, in download_humann2_db subprocess.check_call(cmd, shell=True) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'humann2_databases --download chocophlan full /Users/lplotta/galaxy/database/jobs_directory/000/24/dataset_29_files/chocophlan --update-config no' returned non-zero exit status 127

This happens with both MetaPhlan2 and Humann databases. How can I fix it?

humann database metaphlan • 185 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by lotta.purkamo0
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

These Data Managers are authored by the IUC team. I asked them at their Gitter channel to help troubleshoot the problem.

They might answer back to this post, or you can follow up with them directly at Gitter. The conversation was started here: https://gitter.im/galaxy-iuc/iuc?at=5abd1d1f27c509a774b8d467

You might try upgrading to the most current version of Galaxy as a first pass solution: https://docs.galaxyproject.org/en/master/releases/index.html

If that doesn't resolve the issue, or you are using a Cloudman or Docker Galaxy, please note the version and source in any followup (here or at Gitter).

Sorry you are having problems but this should help to get them resolved.

Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k
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