Loading reads (2023-07-08 00:29:15)
-----------------------------------
38,855 / 38,855 (100.0%) - 254,724,562 bp
Assembling contigs and long reads with miniasm (2023-07-08 00:29:21)
--------------------------------------------------------------------
Saving to /storage/C1231_LRassembly/miniasm_assembly/01_assembly_reads.fastq:
38,855 long reads
Finding overlaps with minimap...
success
5,947,215 overlaps
Assembling reads with miniasm...
success
320 segments, 320 links
Saving /storage/C1231_LRassembly/miniasm_assembly/11_branching_paths_removed.gfa
Merging segments into unitigs:
1 circular unitig
total size = 1,671,271 bp
Saving /storage/C1231_LRassembly/miniasm_assembly/12_unitig_graph.gfa
Saving /storage/C1231_LRassembly/002_unitig_graph.gfa
Polishing miniasm assembly with Racon (2023-07-08 00:32:20)
-----------------------------------------------------------
Unicycler now uses Racon to polish the miniasm assembly. It does multiple rounds of polishing to get the best consensus. Circular unitigs are rotated between rounds such that all parts (including the ends) are polished well.
Saving to /storage/C1231_LRassembly/miniasm_assembly/racon_polish/polishing_reads.fastq:
38,855 long reads
Polish Assembly Mapping
round size quality
begin 1,671,271 29,207.18
1 1,685,412 33,629.12
2 1,685,573 33,654.73
3 1,685,628 33,682.91
Best polish: /storage/C1231_LRassembly/miniasm_assembly/racon_polish/016_rotated.fasta
Saving /storage/C1231_LRassembly/miniasm_assembly/13_racon_polished.gfa
Saving /storage/C1231_LRassembly/003_racon_polished.gfa
Rotating completed replicons (2023-07-08 00:38:35)
--------------------------------------------------
Any completed circular contigs (i.e. single contigs which have one link connecting end to start) can have their start position changed without altering the sequence. For consistency, Unicycler now searches for a starting gene (dnaA or repA) in each such contig, and if one is found, the contig is rotated to start with that gene on the forward strand.
Segment Length Depth Starting gene Position Strand Identity Coverage
1 1,685,628 1.00x none found
2 585,617 1.00x none found
Assembly complete (2023-07-08 00:39:06)
---------------------------------------
Saving /storage/C1231_LRassembly/assembly.gfa
Coloreado en 0.000 segundos, usando
GeSHi 1.0.8.4