4. Logging and intermediary files

Log File Management

During the execution of various commands, it is important to keep track of the user inputs and outputs generated by the software. This is facilitated by the log file repgenr.log, which is automatically stored within the current working directory.

Preserving Intermediary Files

In bioinformatics, it might be necessary to inspect intermediary files for quality control or for in-depth analysis. By default, these files may be cleaned up after the execution of certain modules. However, if you wish to retain these files, such as after running the derep (dereplication) and phylo (phylogenetic analysis) modules, the --keep_files option should be used.

With this option, all intermediary files created during the execution of these modules will be preserved in the working directory. This allows you to revisit any stage of the process for verification or further research.