[2026-03-26 11:02:08] INFO: Starting Flye 2.9.6-b1802
[2026-03-26 11:02:08] INFO: >>>STAGE: configure
[2026-03-26 11:02:08] INFO: Configuring run
[2026-03-26 11:09:59] INFO: Total read length: 66649431823
[2026-03-26 11:09:59] INFO: Input genome size: 2300000000
[2026-03-26 11:09:59] INFO: Estimated coverage: 28
[2026-03-26 11:09:59] INFO: Reads N50/N90: 6713 / 3710
[2026-03-26 11:09:59] INFO: Minimum overlap set to 4000
[2026-03-26 11:09:59] INFO: >>>STAGE: assembly
[2026-03-26 11:09:59] INFO: Assembling disjointigs
[2026-03-26 11:09:59] INFO: Reading sequences
[2026-03-26 11:17:08] INFO: Building minimizer index
[2026-03-26 11:17:08] INFO: Pre-calculating index storage
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[2026-03-26 11:19:28] INFO: Filling index
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[2026-03-26 11:24:22] INFO: Extending reads
[2026-03-26 11:49:23] INFO: Overlap-based coverage: 8
[2026-03-26 11:49:23] INFO: Median overlap divergence: 0.0013369
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[2026-03-30 04:05:28] INFO: Assembled 215827 disjointigs
[2026-03-30 04:05:29] INFO: Generating sequence
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[2026-03-30 04:07:06] INFO: Filtering contained disjointigs
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[2026-03-30 07:42:38] INFO: Contained seqs: 18470
[2026-03-30 07:43:50] INFO: >>>STAGE: consensus
[2026-03-30 07:43:50] INFO: Running Minimap2
[2026-03-30 11:19:21] INFO: Computing consensus
[2026-03-30 12:11:49] INFO: Alignment error rate: 0.009710
[2026-03-30 12:12:09] INFO: >>>STAGE: repeat
[2026-03-30 12:12:09] INFO: Building and resolving repeat graph
[2026-03-30 12:12:10] INFO: Parsing disjointigs
[2026-03-30 12:12:36] INFO: Building repeat graph
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[2026-03-30 17:18:27] INFO: Median overlap divergence: 0.028903
[2026-03-30 18:35:53] INFO: Parsing reads
[2026-03-30 18:43:18] INFO: Aligning reads to the graph
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[2026-03-31 08:13:25] INFO: Aligned read sequence: 52001824379 / 57708191730 (0.901117)
[2026-03-31 08:13:25] INFO: Median overlap divergence: 0.000320852
[2026-03-31 08:13:34] INFO: Mean edge coverage: 12
[2026-03-31 08:13:46] INFO: Simplifying the graph
[2026-03-31 08:22:42] INFO: >>>STAGE: contigger
[2026-03-31 08:22:42] INFO: Generating contigs
[2026-03-31 08:22:43] INFO: Reading sequences
[2026-03-31 08:31:47] INFO: Generated 195061 contigs
[2026-03-31 08:32:08] INFO: Added 867 scaffold connections
[2026-03-31 08:33:38] INFO: >>>STAGE: polishing
[2026-03-31 08:33:38] INFO: Polishing genome (1/1)
[2026-03-31 08:33:38] INFO: Running minimap2
[2026-03-31 12:32:20] INFO: Separating alignment into bubbles
[2026-03-31 13:38:13] INFO: Alignment error rate: 0.016174
[2026-03-31 13:38:13] INFO: Correcting bubbles
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[2026-03-31 17:25:06] INFO: >>>STAGE: finalize
[2026-03-31 17:25:45] INFO: Assembly statistics:

	Total length:	4046369763
	Fragments:	112562
	Fragments N50:	74514
	Largest frg:	2170611
	Scaffolds:	0
	Mean coverage:	15

[2026-03-31 17:25:45] INFO: Final assembly: /mmfs1/gscratch/scrubbed/samwhite/gitrepos/RobertsLab/project-lake-trout/output/13.1-genome-assembly-lean/assembly.fasta