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Create base data directory with pf-construct-genus-data-for-genera This uses pf-build-nr to compute nonredundant databases, and pf-compute-nr-seqs to create sets of sequences corresponding to the reference sequence in the nonredundant sets.
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Use pf-submit-all-local families to start the local fam run.
olson@bio-compute-02:/vol/bvbrc-families/fams/test.2024-1206/genus.data$ rm -r /dev/shm/musc; mkdir -p /dev/shm/musc; time pf-compute-local-family-alignments --parallel 30 Buchnera-32199 ../kmers /dev/shm/musc Buchnera-32199 --overload 1 --aligner mafft
real 7m10.889s user 30m36.985s sys 161m26.406s
muscle
real 11m35.496s user 110m13.439s sys 150m33.937s
muscle 60 proc: real 8m13.195s user 130m38.191s sys 173m23.799s