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CDCgov / legionella_pneumophila_SBT_analysis

Apache License 2.0
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Error during fastqc-1 step #1

Open PHemarajata opened 2 years ago

PHemarajata commented 2 years ago

Hi, I got the following error while trying to run the workflow using test data:

Traceback (most recent call last): File "/usr/games/singularity", line 11, in load_entry_point('Endgame-Singularity==1.0', 'gui_scripts', 'singularity')() File "/usr/lib/python3/dist-packages/singularity/init.py", line 78, in main i18n.set_language(force=True) File "/usr/lib/python3/dist-packages/singularity/code/i18n.py", line 109, in set_language gettext_language = gettext.translation(TEXTDOMAIN_PREFIX + 'messages', _get_main_localedir(), languages=[lang], fallback=True) File "/usr/lib/python3/dist-packages/singularity/code/i18n.py", line 56, in _get_main_localedir main_localedir = dirs.get_writable_file_in_dirs('locale', 'i18n') File "/usr/lib/python3/dist-packages/singularity/code/dirs.py", line 220, in get_writable_file_in_dirs write_dir = write_dirs[dir_name] KeyError: 'i18n'

jennahamlin commented 2 years ago

Hi @PHemarajata

Unfortunately, I don't know how to interpret this error message at the moment. I just tested out the repo via a fresh install following the directions on the README and had success. Did you follow the install steps as listed on the README? If not, what were the commands you tried for installing and running?

jhphan commented 2 years ago

It looks like there's a conflict with 'singularity' on your machine. Unfortunately on Ubuntu and Debian, there's a package called 'singularity' that's actually a game. It conflicts with the 'singularity-container' package. Try uninstalling 'singularity' first, if that doesn't resolve it, then try reinstalling singularity-container.

PHemarajata commented 2 years ago

Hi! I tried the method @jhphan suggested and it worked. Thank you so much!