Starting Trycycler MSA (2020-07-06 14:18:27)
    Trycycler MSA is a tool for conducting global multiple sequence alignment
of contig sequences.

Input sequences:
  A_contig_1: 1,044,291 bp
  B_contig_1: 1,044,295 bp
  C_contig_1: 1,044,313 bp
  D_contig_1: 1,044,336 bp
  E_contig_1: 1,044,318 bp
  F_utg000001c: 1,044,419 bp
  G_utg000001c: 1,044,418 bp
  H_utg000001c: 1,044,435 bp
  I_utg000001c: 1,044,409 bp
  J_utg000001c: 1,044,416 bp

Checking required software:
   MUSCLE: v3.8.1551


Partitioning sequences (2020-07-06 14:18:27)
    The sequences are now partitioned into smaller chunks to make the multiple
sequence alignment more tractable.

pieces: 1025

median piece size: 1,000 bp
max piece size:    3,000 bp


Running Muscle (2020-07-06 14:18:41)
    Trycycler now runs Muscle on each of the pieces to turn them into multiple
sequence alignments.

pieces: 1025


Merging MSA (2020-07-06 14:19:54)
    Each of the MSA pieces are now merged together and saved to file.

MSA length: 1,044,540 bp
Saving to: trycycler/cluster_001/3_msa.fasta