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Use cases
If you want to compute the core ortholog groups only (step 1 in the fDOG workflow), you can just skip the other downstream steps by using the option --coreOnly
fdog.run --seqFile infile.fa --jobName test --refspec HUMAN@9606@3 --coreOnly
In case you don't want to use the FAS scores to select candidates for the core group members, you can turn off the FAS score evaluation of the core compilation
fdog.run --seqFile infile.fa --jobName test --refspec HUMAN@9606@3 --coreOnly --fasoff
You already have the core ortholog group for your seed protein, you can directly use it for the ortholog search
fdog.run --seqFile infile.fa --jobName test --refspec HUMAN@9606@3 --reuseCore
In this case, fDOG will find the corresponding core ortholog group in the core_orthologs folder (can be defined by the option --hmmpath) that is named test (specified by the option --jobName). Therefore, if you encounter any problem of not finding the core group, please check if the directory core_orthologs/test/ exists and if its contain is as expected (i.e. it must contain a test.fa file where all core sequences can be found, as well as its profile HMM in hmm_dir/test.hmm file).
NOTE: If you don't have the seed file infile.fa, you can use directly the fasta file core_orthologs/test/test.fa for the --seqFile option. Or, you can manually create a pseudo.fa file and use it as your seed file ^_^