Running: ../LINKS [v1.0]
-f ecoli-6.fa
-s K12_full2dONT_longread.fa
-d 4000
-k 15
-e 0.1
-l 5
-a 0.3
-t 2
-p 0

=>Reading long reads initiated: Mon Apr 13 09:02:37 PDT 2015

=>Reading sequence contigs (to scaffold) initiated: Mon Apr 13 09:02:37 PDT 2015

=>Scaffolding initiated: Mon Apr 13 09:03:03 PDT 2015

===========PAIRED K-MER STATS===========
Total number of pairs extracted from -s K12_full2dONT_longread.fa: 4891397
At least one sequence/pair missing from contigs: 0
Assembled pairs: 68363 (136726 sequences)
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 54722
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 579
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 303
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 662
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 12097
	---
Total satisfied: 55384	unsatisfied: 12979

Breakdown by insert sizes:
--------Reads with 4000 bp inserts--------
MIN:3600 MAX:4400 as defined by 4000 * 0.1
At least one sequence/pair missing: 
Assembled pairs: 68363
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 54722
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 579
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 303
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 662
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 12097
============================================
=>Scaffolding ended: Mon Apr 13 09:03:27 PDT 2015
=>Making fasta file: Mon Apr 13 09:03:27 PDT 2015