Starting Trycycler partitioning (2020-07-06 14:22:06)
    Trycycler partition is a tool for partitioning reads by cluster. I.e. each
read will be assigned to one cluster and saved in a file for that cluster.

Input reads: reads.fastq.gz
  43,662 reads (210,403,674 bp)
  N50 = 7,768 bp

Input clusters:
  trycycler/cluster_001/2_all_seqs.fasta: 10 contigs, mean length = 1,044,365 bp
  trycycler/cluster_002/2_all_seqs.fasta: 10 contigs, mean length = 7,509 bp

Checking required software:
  minimap2: v2.17-r954-dirty


Aligning reads to each contig (2020-07-06 14:22:09)
    The reads are independently aligned to each of the contigs and Trycycler
will remember the single best alignment for each read.

  A_contig_1 (1,044,291 bp): 39,801 alignments
  B_contig_1 (1,044,295 bp): 39,800 alignments
  C_contig_1 (1,044,313 bp): 39,801 alignments
  D_contig_1 (1,044,336 bp): 39,800 alignments
  E_contig_1 (1,044,318 bp): 39,803 alignments
F_utg000001c (1,044,419 bp): 39,800 alignments
G_utg000001c (1,044,418 bp): 39,802 alignments
H_utg000001c (1,044,435 bp): 39,800 alignments
I_utg000001c (1,044,409 bp): 39,800 alignments
J_utg000001c (1,044,416 bp): 39,800 alignments

  A_contig_2 (7,504 bp): 3,043 alignments
  B_contig_2 (7,509 bp): 3,044 alignments
  C_contig_2 (7,512 bp): 3,044 alignments
  D_contig_2 (7,508 bp): 3,044 alignments
  E_contig_2 (7,508 bp): 3,044 alignments
F_utg000002c (7,523 bp): 3,045 alignments
G_utg000002c (7,509 bp): 3,043 alignments
H_utg000002c (7,509 bp): 3,041 alignments
I_utg000002c (7,506 bp): 3,042 alignments
J_utg000002c (7,511 bp): 3,045 alignments


Saving reads to cluster directories (2020-07-06 14:23:36)
    Reads are now saved in a file in the cluster directory to which they
aligned best.

trycycler/cluster_001/4_reads.fastq:
  31,959 reads (73.20%)
  192,572,569 bases (91.53%)

trycycler/cluster_002/4_reads.fastq:
  2,229 reads (5.11%)
  10,440,509 bases (4.96%)