Running: ../LINKS [v1.5]
-f ecoliK12_abyss_illumina_scaffold_baseline.fa
-s K12_F2D.fof
-d 4000
-k 15
-e 0.1
-l 5
-a 0.3
-t 2
-o 0
-b ecoliK12-ONT_linksSingleIterationSCAFF
-r 
-g 0

Checking K12_full2dONT_longread.fa...ok
Checking sequence target file ecoliK12_abyss_illumina_scaffold_baseline.fa...ok

=>Reading contigs file, building Bloom filter: Mon Apr 27 13:46:06 PDT 2015

Contigs processed k=15:
63


=>Writing Bloom filter to disk (ecoliK12-ONT_linksSingleIterationSCAFF.bloom): Mon Apr 27 13:47:01 PDT 2015

=>Reading long reads, building hash table: Mon Apr 27 13:47:01 PDT 2015

Reads processed k=15, dist=4000, offset=0 nt, sliding step=2 nt:

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


Extracted 81384 total 15-mer pairs

=>Reading sequence contigs (to scaffold), tracking k-mer positions: Mon Apr 27 13:47:20 PDT 2015

Contigs processed k=15:
63


=>Scaffolding initiated: Mon Apr 27 13:47:26 PDT 2015

===========PAIRED K-MER STATS===========
Total number of pairs extracted from -s K12_F2D.fof: 81384
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: 54953
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 622
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 349
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 406
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 12033
	---
Total satisfied: 55359	unsatisfied: 13004

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: 54953
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 622
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 349
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 406
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 12033
============================================
=>Scaffolding ended: Mon Apr 27 13:47:33 PDT 2015
=>Making FASTA file: Mon Apr 27 13:47:33 PDT 2015

Scaffolding executed normally Mon Apr 27 13:47:36 PDT 2015