- 'logs' directory: Contains the job submission standard output and standard error files generated by iPlant CyVerse systems. Usually this will only be important for troubleshooting if your job does not run.
- 'OrthoMCL_homolog_clustering_workflow_example.conf' file: Contains a record of the input files and parameters used. Use this to verify that your run executed as you intended. Some of this information is duplicated in files below, but is presented at this level for ease of use.
- 'OrthoMCL_homolog_clustering_workflow_example.log' file: Contains a log record of OrthoMCL output. This contains valuable information for you to ensure that the correct number of species and sequences went into the analysis and to see how many clusters were generated. While some lines of the file may not be meaningful to you, it is worth your time to have a look at this file as part of examining your output. Some of this information is duplicated in files below, but is presented at this level for ease of use.
- 'parsedBLASToutput_bpo.txt_bpo.idx': Contains OrthoMCL's index of the input BPO file. Unless you have a specific interest, you can ignore this file.
- 'Nov_14' directory: Contains the main program output and other accessory files needed for downstream processing in the Cluster Orthologs and Paralogs and Assemble Custom Gene Sets workflow.
- 'all_orthomcl.out' file: This is the main output file for the program. Each line of the text file contains an OrthoMCL cluster, ie a set of genes detected as evolutionarily related orthologs and paralogs. Each line begins with an arbitrary ID followed by the number of genes and number of taxa in that cluster, followed by a list of gene IDs and 2-letter taxa abbreviations chosen in the Cluster Orthologs and Paralogs and Assemble Custom Gene Sets workflow. The number of lines in this file should match the number of clusters generated, recorded in the OrthoMCL_homolog_clustering_workflow_example.log file. For example, consider cluster number 610 from the example all_orthomcl.out file