...
The naming of these directories is important, as the CRUX script automatically looks in the /crux_db/Obitools_databases directory for any databases beginning with OB_dat_.
Run the obiconvert command from the anacapa Singularity image.
| Code Block |
|---|
singularity exec ~/anacapa/anacapa-1.5.0.img obiconvert -t ~/anacapa/crux_db/TAXO --embl --ecopcrdb-output=~/anacapa/crux_db/Obitools_databases/OB_dat_EMBL_std/OB_dat_EMBL_std ~/anacapa/crux_db/EMBL/*.dat --skip-on-error |
This uses the NCBI taxonomy database (downloaded to ~/anacapa/crux_db/TAXO) and the EMBL database (downloaded to ~/anacapa/crux_db/EMBL/*.dat) and it outputs the ecoPCR converted database to /Obitools_databases/OB_dat_EMBL_std/ and prepends the generated ecoPCR database files with OB_dat_EMBL_std....
Cleanup
Running the anacapa workflow involves downloading and generating various large databases. These will just take up space on the HPC unless removed.
...