Reconcile fails when fasta files

[erinyoung]

My apologies for using Trycycler slightly differently than the tutorial.

I created 12 assemblies for an isolate followed by some polishing and circlator (if the sequences were circular).

This created 12 assemblies with the same start and stop, which causes Trycycler to fail at the reconcile step.

Circularising A_1:
  using B_1:
    unable to circularise: A_1's start/end is the same as B_1's start/end
  using C_1:
    unable to circularise: A_1's start/end is the same as C_1's start/end
  using D_Utg634:
    unable to circularise: A_1's start/end is the same as D_Utg634's start/end
  using E_utg000001c:
    unable to circularise: A_1's start/end is the same as E_utg000001c's start/end
  using F_utg000001c:
    unable to circularise: A_1's start/end is the same as F_utg000001c's start/end
  using G_Utg550:
    unable to circularise: A_1's start/end is the same as G_Utg550's start/end
  using H_Utg602:
    unable to circularise: A_1's start/end is the same as H_Utg602's start/end
  using I_utg000001c:
    unable to circularise: A_1's start/end is the same as I_utg000001c's start/end
  using J_edge_1:
    unable to circularise: A_1's start/end is the same as J_edge_1's start/end
  using K_edge_1:
    unable to circularise: A_1's start/end is the same as K_edge_1's start/end
  using L_edge_1:
    unable to circularise: A_1's start/end is the same as L_edge_1's start/end

Is there any way to turn this flag off?

[rrwick]

Hi Erin,

If you've already circularised your input assemblies (same starts/ends), then you can tell Trycycler to treat the cluster as a linear replicon with --linear. This will make it skip the circularisation steps.

Ryan