Anacapa is a toolkit designed to construct reference databases and assign taxonomy, from eDNA sequences.
...
| Code Block |
|---|
mkdir -p ~/anacapa/crux_db/Obitools_databases/OB_dat_120322_EMBL_std_mam |
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.
...
Important: You need to change every instance of /home/your_home_directory in the below command to your actual home directory (this is because obiconvert requires absolute paths). To find your home directory path, type cd ~ and then pwd. Use the path that this displays to replace the /home/your_home_directory.
| Code Block |
|---|
singularity exec /home/your_home_directory/anacapa/anacapa-1.5.0.img obiconvert -t ~/home/your_home_directory/anacapa/crux_db/TAXO --embl --ecopcrdb-output=~/home/your_home_directory/anacapa/crux_db/Obitools_databases/OB_dat_120322_EMBL_std_mam/OB_dat_120322_EMBL_std_mam ~ /home/your_home_directory/anacapa/crux_db/EMBL/*.dat --skip-on-error |
This The above obiconvert command 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....
...