Starting Trycycler reconcile (2020-07-08 15:17:10)
    Trycycler reconcile is a tool for reconciling multiple alternative contigs
with each other.

Input reads: reads.fastq.gz
  size = 216,254,308 bytes

Input contigs:
  trycycler/cluster_002/1_contigs/A_contig_10.fasta (7,455 bp)
  trycycler/cluster_002/1_contigs/B_contig_8.fasta (7,455 bp)
  trycycler/cluster_002/1_contigs/C_contig_4.fasta (7,535 bp)
  trycycler/cluster_002/1_contigs/D_contig_2.fasta (14,941 bp)
  trycycler/cluster_002/1_contigs/E_contig_18.fasta (7,450 bp)

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


Initial check of contigs (2020-07-08 15:17:10)
    Before proceeding, Trycycler ensures that the input contigs appear
sufficiently close to each other to make a consensus. If not, the program will
quit and the user must fix the input contigs (make them more similar to each
other) or exclude some before trying again.

Relative sequence lengths:
  A_contig_10: 1.000  1.000  0.989  0.499  1.001
  B_contig_8:  1.000  1.000  0.989  0.499  1.001
  C_contig_4:  1.011  1.011  1.000  0.504  1.011
  D_contig_2:  2.004  2.004  1.983  1.000  2.006
  E_contig_18: 0.999  0.999  0.989  0.499  1.000


Error: there is too much length difference between contigs. You must either
exclude or repair the offending contig sequences and then try running trycycler
reconcile again. If one of the sequences is too long, it could be due to
excessive circularisation overlap, and trimming that overlap may allow
trycycler reconcile to continue.