Running: /genesis/extscratch/btl/rwarren/long_scaffolding/spruce/LINKS [v1.0]
-f links13.scaffolds.fa
-s ws77111sealed1_500.fa
-d 100000
-k 26
-e 0.1
-l 5
-a 0.3
-t 50
-p 0

=>Reading long reads initiated: Mon Jan  5 10:28:21 PST 2015

=>Reading sequence contigs (to scaffold) initiated: Mon Jan  5 10:28:21 PST 2015

=>Scaffolding initiated: Tue Jan  6 01:20:48 PST 2015

===========PAIRED K-MER STATS===========
Total number of pairs extracted from -s ws77111sealed1_500.fa: 77158206
At least one sequence/pair missing from contigs: 0
Assembled pairs: 2393079 (4786158 sequences)
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 880539
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 335959
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 3718
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 327692
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 845171
	---
Total satisfied: 1208231	unsatisfied: 1184848

Breakdown by insert sizes:
--------Reads with 100000 bp inserts--------
MIN:90000 MAX:110000 as defined by 100000 * 0.1
At least one sequence/pair missing: 
Assembled pairs: 2393079
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 880539
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 335959
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 3718
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 327692
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 845171
============================================
=>Scaffolding ended: Tue Jan  6 01:26:54 PST 2015
=>Making fasta file: Tue Jan  6 01:26:55 PST 2015