Running: ../LINKS [v1.5]
-f RK12links29.scaffolds.fa
-s K12_R.fof
-d 16000
-k 15
-e 0.1
-l 5
-a 0.3
-t 2
-o 0
-b RK12links30
-r RK12links1.bloom
-g 0

Checking K12_rawONT_longread.fa...ok
Checking sequence target file RK12links29.scaffolds.fa...ok

=>Reading contigs file, building Bloom filter: Mon Apr 27 16:47:03 PDT 2015
Checking Bloom filter file RK12links1.bloom...ok
A Bloom filter was supplied (RK12links1.bloom) and will be used instead of building a new one from -f RK12links29.scaffolds.fa

=>Reading long reads, building hash table: Mon Apr 27 16:47:03 PDT 2015

Reads processed k=15, dist=16000, offset=0 nt, sliding step=2 nt:

Reads processed from file 1/1, K12_rawONT_longread.fa:
70531


Extracted 1400 total 15-mer pairs

=>Reading sequence contigs (to scaffold), tracking k-mer positions: Mon Apr 27 16:47:10 PDT 2015

Contigs processed k=15:
28


=>Scaffolding initiated: Mon Apr 27 16:47:13 PDT 2015

===========PAIRED K-MER STATS===========
Total number of pairs extracted from -s K12_R.fof: 1400
At least one sequence/pair missing from contigs: 0
Assembled pairs: 1175 (2350 sequences)
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 727
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 59
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 58
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 1
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 330
	---
Total satisfied: 728	unsatisfied: 447

Breakdown by insert sizes:
--------Reads with 16000 bp inserts--------
MIN:14400 MAX:17600 as defined by 16000 * 0.1
At least one sequence/pair missing: 
Assembled pairs: 1175
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 727
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 59
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 58
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 1
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 330
============================================
=>Scaffolding ended: Mon Apr 27 16:47:15 PDT 2015
=>Making FASTA file: Mon Apr 27 16:47:15 PDT 2015

Scaffolding executed normally Mon Apr 27 16:47:16 PDT 2015