The usage and help documentation of extract_fasta_bins.py can be seen by running extract_fasta_bins.py -h:

usage: - [-h] [--output_path OUTPUT_PATH] fasta_file cluster_file

extract_fasta_bins.py Extract a fasta file for each cluster from a concoct
result file.

positional arguments:
  fasta_file            Input Fasta file.
  cluster_file          Concoct output cluster file

optional arguments:
  -h, --help            show this help message and exit
  --output_path OUTPUT_PATH
                        Directory where files will be printed


An example of how to run extract_fasta_bins.py:

mkdir concoct_output/fasta_bins
extract_fasta_bins.py original_contigs.fa concoct_output/clustering_merged.csv --output_path concoct_output/fasta_bins

This creates a fasta file for each cluster assigned by concoct. The clusters assigned need not to be complete or uncontaminated and should be investigated closer with e.g. CheckM.