06_PROFILES

Step 1. Activate the Anvio environment

Step 2. Had to migrate the contig databases to

# cd into the 04_CONTIGS/ directory
# migrate the databases
anvi-migrate *.db --migrate-dbs-quickly

Step 3. Profiling of samples

Perform a nested loop as was done for the mapping step. Do not try to parallelize this! Anvio-profile gets confused if you try to start multiple processes for this at once.

conda activate anvio_emily

while read line;      
    do         
    SET=$(echo $line | cut -d" " -f1);          
    samples=$(echo $line | cut -d" " -f2);          
    delimiter=",";          
    declare -a Smparray=($(echo $samples | tr "$delimiter" " "));         
    for samp in "${Smparray[@]}"; 
        do
            anvi-profile -c 04_CONTIGS/$SET-CONTIGS.db \
            -i 05_MAPPING/$samp.bam \
            --skip-SNV-profiling \
            --num-threads 40 \
            -o 06_PROFILES/$samp
        done;     
    done < samples_in_sets.txt