Anacapa is a toolkit designed to construct reference databases and assign taxonomy, from eDNA sequences.
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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.
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#!/bin/bash -l
#PBS -N ObiRun
#PBS -l select=1:ncpus=2:mem=64gb
#PBS -l walltime=96:00:00
cd $PBS_O_WORKDIR
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_EMBL_std/OB_dat_EMBL_std \
--skip-on-error \
/home/your_home_directory/anacapa/crux_db/EMBL/*.dat |
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The -d should point to where your CRUX databases are. Check in this directory. You should see subdirectories containing NCBI taxonomy, obiconvert results, NCBI accession2taxonomy databases (see ‘Step 3: Create reference libraries using CRUX’ to see where you created these databases).
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#!/bin/bash -l
#PBS -N CRUX
#PBS -l select=1:ncpus=2:mem=64gb
#PBS -l walltime=24:00:00
cd $PBS_O_WORKDIR
singularity exec docker://ghcr.io/eresearchqut/anacapa-image:0.0.3 /bin/bash \
/home/your_home_directory/anacapa/crux_db/crux.sh \
-n 16Smam -f CGGTTGGGGTGACCTCGGA -r GCTGTTATCCCTAGGGTAACT \
-s 40 -m 240 \
-o /home/your_home_directory/anacapa/16Smam \
-d /home/your_home_directory/anacapa/crux_db/ -l |
Step 5: Running anacapa
Now that the CRUX databases have been constructed, we can run anacapa itself on these databases.
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