neherlab/pan-genome-analysis

Step for generation of archive all_protein_seq.cpk

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I have the question of when is the archive all_protein_seq.cpk generated. Because if I run the steps one by one this archive is not generated. and when I want to run the step 6 naturally doesn't work.
When I run all the steps at the same time in step 5 broken because the archives .faa disapear. and said that there is not .faa archives.
Thanks in advance.