Running: ../LINKS [v1.5]
-f K12links29.scaffolds.fa
-s K12_F2D.fof
-d 16000
-k 15
-e 0.1
-l 5
-a 0.3
-t 2
-o 0
-b K12links30
-r K12links1.bloom
-g 0

Checking K12_full2dONT_longread.fa...ok
Checking sequence target file K12links29.scaffolds.fa...ok

=>Reading contigs file, building Bloom filter: Mon Apr 27 18:17:18 PDT 2015
Checking Bloom filter file K12links1.bloom...ok
A Bloom filter was supplied (K12links1.bloom) and will be used instead of building a new one from -f K12links29.scaffolds.fa

=>Reading long reads, building hash table: Mon Apr 27 18:17:18 PDT 2015

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

Reads processed from file 1/1, K12_full2dONT_longread.fa:
3471


Extracted 1459 total 15-mer pairs

=>Reading sequence contigs (to scaffold), tracking k-mer positions: Mon Apr 27 18:17:19 PDT 2015

Contigs processed k=15:
29


=>Scaffolding initiated: Mon Apr 27 18:17:22 PDT 2015

===========PAIRED K-MER STATS===========
Total number of pairs extracted from -s K12_F2D.fof: 1459
At least one sequence/pair missing from contigs: 0
Assembled pairs: 1233 (2466 sequences)
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 976
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 13
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 20
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 0
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 224
	---
Total satisfied: 976	unsatisfied: 257

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: 1233
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 976
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 13
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 20
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 224
============================================
=>Scaffolding ended: Mon Apr 27 18:17:22 PDT 2015
=>Making FASTA file: Mon Apr 27 18:17:22 PDT 2015

Scaffolding executed normally Mon Apr 27 18:17:22 PDT 2015