Running: ../LINKS [v1.5]
-f STH58links10.scaffolds.fa
-s STH58_2D.fof
-d 4000
-k 15
-e 0.1
-l 5
-a 0.1
-t 1
-o 0
-b STH58links11
-r STH58links1.bloom
-g 0

Checking StyphiH58_2dONT_longread.fa...ok
Checking sequence target file STH58links10.scaffolds.fa...ok

=>Reading contigs file, building Bloom filter: Mon Apr 27 17:58:29 PDT 2015
Checking Bloom filter file STH58links1.bloom...ok
A Bloom filter was supplied (STH58links1.bloom) and will be used instead of building a new one from -f STH58links10.scaffolds.fa

=>Reading long reads, building hash table: Mon Apr 27 17:58:29 PDT 2015

Reads processed k=15, dist=4000, offset=0 nt, sliding step=1 nt:

Reads processed from file 1/1, StyphiH58_2dONT_longread.fa:
3738


Extracted 95186 total 15-mer pairs

=>Reading sequence contigs (to scaffold), tracking k-mer positions: Mon Apr 27 17:59:04 PDT 2015

Contigs processed k=15:
65


=>Scaffolding initiated: Mon Apr 27 17:59:10 PDT 2015

===========PAIRED K-MER STATS===========
Total number of pairs extracted from -s STH58_2D.fof: 95186
At least one sequence/pair missing from contigs: 0
Assembled pairs: 87377 (174754 sequences)
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 64581
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 3731
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 1845
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 74
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 17146
	---
Total satisfied: 64655	unsatisfied: 22722

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: 87377
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 64581
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 3731
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 1845
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 74
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 17146
============================================
=>Scaffolding ended: Mon Apr 27 17:59:24 PDT 2015
=>Making FASTA file: Mon Apr 27 17:59:24 PDT 2015

Scaffolding executed normally Mon Apr 27 17:59:31 PDT 2015