Starting Trycycler MSA (2020-07-07 09:52:59)
    Trycycler MSA is a tool for conducting global multiple sequence alignment
of contig sequences.

Input sequences:
  A_contig_1: 1,038,291 bp
  B_contig_2: 1,038,269 bp
  C_contig_1: 1,038,379 bp
  D_contig_1: 1,038,384 bp
  E_contig_1: 1,038,433 bp
  G_utg000001c: 1,042,913 bp
  H_utg000001c: 1,042,821 bp
  I_utg000001c: 1,042,871 bp
  J_utg000001c: 1,042,500 bp

Checking required software:
   MUSCLE: v3.8.1551


Partitioning sequences (2020-07-07 09:52:59)
    The sequences are now partitioned into smaller chunks to make the multiple
sequence alignment more tractable.

pieces: 719

median piece size: 1,000 bp
max piece size:    7,000 bp


Running Muscle (2020-07-07 09:53:12)
    Trycycler now runs Muscle on each of the pieces to turn them into multiple
sequence alignments.

pieces: 719


Merging MSA (2020-07-07 09:56:45)
    Each of the MSA pieces are now merged together and saved to file.

MSA length: 1,046,326 bp
Saving to: trycycler/cluster_001/3_msa.fasta