Starting Trycycler consensus (2020-07-06 14:24:55)
    Trycycler consensus is the final stage of the Trycycler pipeline. It
operates on one replicon (i.e. cluster) at a time. It takes the multiple
sequence alignment of alternative contig sequences and combines them into a
single consensus sequence. Where needed, it will use read alignments to help
choose which variants to include/exclude from the consensus sequence. If all
goes well, the final consensus will be free of any large-scale errors.

Input reads: trycycler/cluster_001/4_reads.fastq
  31,959 reads (192,572,569 bp)
  N50 = 8,431 bp

Input contigs: trycycler/cluster_001/2_all_seqs.fasta
  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:
  minimap2: v2.17-r954-dirty


Partitioning MSA (2020-07-06 14:24:55)
    The multiple sequence alignment is now partitioned into chunks. Chunks
where the input contig sequences are all in agreement are called "same" chunks,
and those where the input contig sequences disagree are called "different"
chunks. The consensus sequence will be made by choosing a best option for each
of the different chunks.

chunks: 1,403 (702 same, 701 different)
combining small chunks: 1,285 (643 same, 642 different)

Saving sequences to graph: trycycler/cluster_001/5_chunked_sequence.gfa


Initial consensus (2020-07-06 14:24:58)
    Trycycler now makes an initial consensus sequence by choosing a sequence
for each of the different chunks. The chosen sequence is the one with the
lowest total Hamming distance to the other sequences. For example, a chunk with
options of TT, TT, CC, CC and TA will give a consensus of TT. If the total
Hamming distances fail to break a tie or if all sequences differ, the chunk
will be flagged for read-based assessment.

Consensus length: 1,044,449 bp

Different chunks needing assessment:     9
Different chunks not needing assessment: 633

Saving sequence to file: trycycler/cluster_001/6_initial_consensus.fasta


Indexing reads (2020-07-06 14:24:58)
    Trycycler now aligns all reads to the initial consensus to form an index of
which reads span each of the chunks. This makes the following step faster, as
only relevant reads will be used when conducting read-based assessment of
chunks.

Aligning reads to the initial consensus:
  32,130 alignments

Filtering for best alignment per read:
  31,959 alignments

Gathering reads for chunks: 9 / 9


Choosing best options with reads (2020-07-06 14:25:17)
    For each of the chunks to be assessed, Trycycler now aligns the relevant
reads to each alternative sequence. Whichever option gives the strongest read
alignments (defined as the total alignment score for each of the read's best
alignment) is chosen as the best. This should result in a consensus sequence
which is more accurate than the initial consensus.

Processing chunks: 9 / 9

Chunks where sequence is...
  the same as in the initial consensus: 1
  different to the initial consensus:   8

Saving sequence to file: trycycler/cluster_001/7_final_consensus.fasta