Example cases

We provide two example cases in the folder examples in this repo. We have already provided the cblaster output files as well as the original query fasta.

Example case 1

In the first case, 1146 gene cluster hits from Staphylococcus spp. should be reduced to 22 non-redundant hits. Running the cagecleaner for this example is done like below

cd N398V589S066P61
cagecleaner -s session.json -o output -c 20

This should give the seven output files in a new subfolder output. This should take about 10' using 20 cores, depending on the download speed of your internet connection. This requires 1.2 GB of disk space and 1.7 GB of RAM.

$ dir -1 output
clusters.txt
filtered_binary.txt
filtered_session.txt
filtered_summary.txt
genome_cluster_sizes.txt
genome_cluster_status.txt
scaffold_assembly_pairs.txt

Example case 2

In the second case, we queried four genes from MIBiG entry BGC0000194 (actinorhodin from Streptomyces coelicolor A3(2)), which yielded 8934 gene cluster hits. cagecleaner should reduce this to 4847 hits in about 1.5 h using 20 cores. 28.5 GB of disk space and 27.6 GB of RAM are required for this example case.

cd actinorhodin
cagecleaner -s session.json -o output -c 20