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- 'logs' directory: Contains the job submission standard output and standard error files generated by iPlant systemsCyVerse systems. Usually this will only be important for troubleshooting if your job does not run.
- unclustered_Added directory contains 3 output files
- appendUnclustered.log records the number of clusters and sequences that the app processed, and the number of sequences, sequences that were clustered, and sequences that were not clustered for each species.
- orthomcl.index and orthomcl.mclout contain the updated MCL output with the included unclustered sequences. These files are not meant to be useful at this stage of the Cluster Orthologs and Paralogs and Assemble Custom Gene Sets app.