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nmquijada / tormes

Making whole bacterial genome sequencing data analysis easy
GNU General Public License v3.0
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kraken2 does not generate any result due to wrong PATH to its database in config_file.txt #30

Closed nmquijada closed 4 years ago

nmquijada commented 4 years ago

There is a bug in tormes-setup while generating the PATH for the kraken2 database in the config_file.txt. If you are not using your own kraken2 database, just the one installed by default in TORMES, please type the following commands to solve this issue:

conda activate tormes-1.2.0 #skip in case the environment is already loaded
sed -i "s/minikraken_8GB_202003$/minikraken_8GB_20200312/" $(which tormes | sed "s/bin\/tormes/files\/config_file.txt/")

This issue will be solved in the next TORMES release. Sorry for the inconveniences. Narciso

nmquijada commented 4 years ago

Fixed in version 1.2.1

Panchastico commented 1 year ago

This may work for version 1.3.0 as well. I have the same problema in version 1.3.0

nmquijada commented 1 year ago

Hi @Panchastico Thanks for sharing! Did you have the same problem in version 1.3.0? That is weird as I corrected the error in version 1.2.1 and I just checked today the database and they still have the same nomenclature... In any case, the config_file.txt records paths, so you can edit it as much as you need (in case you have a different or newer database, etc.) Best, Narciso