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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singularity exec /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/anacapa-1.5.0.img /bin/bash /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/anacapa/Anacapa_db/anacapa_QC_dada2.sh -i /home/whatmorp/nextflow/pia_eDNAFlow/fastq -o /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/16Smam_anacapa_output -d /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/anacapa/Anacapa_db -a nextera -t MiSeq -g -l

Step 6: Running anacapa classifier

Example:

/bin/bash ~/Anacapa_db/anacapa_classifier.sh -o <out_dir_for_anacapa_QC_run> -d <database_directory> -u <hoffman_account_user_name> -l

Required Arguments:

        -o      path to output directory generated in the Sequence QC and ASV Parsing script

        -d      path to Anacapa_db

singularity exec /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/anacapa-1.5.0.img /bin/bash /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/anacapa/Anacapa_db/anacapa_classifier.sh -o /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/16Smam_anacapa_output -d /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/anacapa/Anacapa_db -l

Cleanup

Running the anacapa workflow involves downloading and generating various large databases. These will just take up space on the HPC unless removed.

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