[2020-09-17 09:25:29] INFO: Starting Flye 2.8.1-b1676
[2020-09-17 09:25:29] INFO: >>>STAGE: configure
[2020-09-17 09:25:29] INFO: Configuring run
[2020-09-17 09:25:36] INFO: Total read length: 1154162685
[2020-09-17 09:25:36] INFO: Reads N50/N90: 4923 / 837
[2020-09-17 09:25:36] INFO: Minimum overlap set to 1000
[2020-09-17 09:25:36] INFO: >>>STAGE: assembly
[2020-09-17 09:25:36] INFO: Assembling disjointigs
[2020-09-17 09:25:36] INFO: Reading sequences
[2020-09-17 09:25:46] INFO: Counting k-mers:
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[2020-09-17 09:27:34] INFO: Filling index table (1/2)
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[2020-09-17 09:27:51] INFO: Filling index table (2/2)
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[2020-09-17 09:28:27] INFO: Extending reads
[2020-09-17 09:29:53] INFO: Overlap-based coverage: 2
[2020-09-17 09:29:53] INFO: Median overlap divergence: 0.128899
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[2020-09-17 09:42:45] INFO: Assembled 1392 disjointigs
[2020-09-17 09:42:46] INFO: Generating sequence
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[2020-09-17 09:42:49] INFO: >>>STAGE: consensus
[2020-09-17 09:42:50] INFO: Running Minimap2
[2020-09-17 09:48:02] INFO: Computing consensus
[2020-09-17 09:55:15] INFO: Alignment error rate: 0.113597
[2020-09-17 09:55:15] INFO: >>>STAGE: repeat
[2020-09-17 09:55:15] INFO: Building and resolving repeat graph
[2020-09-17 09:55:15] INFO: Parsing disjointigs
[2020-09-17 09:55:16] INFO: Building repeat graph
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[2020-09-17 09:58:28] INFO: Median overlap divergence: 0.0879
[2020-09-17 09:58:36] INFO: Parsing reads
[2020-09-17 09:58:43] INFO: Aligning reads to the graph
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[2020-09-17 10:02:35] INFO: Aligned read sequence: 598922529 / 1011373375 (0.592187)
[2020-09-17 10:02:35] INFO: Median overlap divergence: 0.0782493
[2020-09-17 10:02:35] INFO: Mean edge coverage: 34
[2020-09-17 10:02:36] INFO: Simplifying the graph
[2020-09-17 10:04:40] INFO: >>>STAGE: contigger
[2020-09-17 10:04:40] INFO: Generating contigs
[2020-09-17 10:04:40] INFO: Reading sequences
[2020-09-17 10:04:56] INFO: Generated 3513 contigs
[2020-09-17 10:04:57] INFO: Added 6 scaffold connections
[2020-09-17 10:16:35] INFO: >>>STAGE: polishing
[2020-09-17 10:16:35] INFO: Polishing genome (1/1)
[2020-09-17 10:16:35] INFO: Running minimap2
[2020-09-17 10:21:10] INFO: Separating alignment into bubbles
[2020-09-17 10:31:47] INFO: Alignment error rate: 0.120815
[2020-09-17 10:31:47] INFO: Correcting bubbles
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[2020-09-17 10:36:24] INFO: >>>STAGE: finalize
[2020-09-17 10:36:25] INFO: Assembly statistics:

	Total length:	19216531
	Fragments:	3294
	Fragments N50:	14130
	Largest frg:	141601
	Scaffolds:	6
	Mean coverage:	17

[2020-09-17 10:36:25] INFO: Final assembly: /gscratch/scrubbed/samwhite/outputs/20200915_cbai_flye_nanopore_genome_assembly/assembly.fasta