Running: ../LINKS [v1.5]
-f S288clinks28.scaffolds.fa
-s W303_RAW.fof
-d 16000
-k 15
-e 0.1
-l 5
-a 0.3
-t 6
-o 0
-b S288clinks29
-r S288clinks1.bloom
-g 0

Checking W303_rawONT_longread.fa...ok
Checking sequence target file S288clinks28.scaffolds.fa...ok

=>Reading contigs file, building Bloom filter: Mon Apr 27 23:42:42 PDT 2015
Checking Bloom filter file S288clinks1.bloom...ok
A Bloom filter was supplied (S288clinks1.bloom) and will be used instead of building a new one from -f S288clinks28.scaffolds.fa

=>Reading long reads, building hash table: Mon Apr 27 23:42:42 PDT 2015

Reads processed k=15, dist=16000, offset=0 nt, sliding step=6 nt:

Reads processed from file 1/1, W303_rawONT_longread.fa:
262463


Extracted 14985 total 15-mer pairs

=>Reading sequence contigs (to scaffold), tracking k-mer positions: Mon Apr 27 23:43:21 PDT 2015

Contigs processed k=15:
8447


=>Scaffolding initiated: Mon Apr 27 23:43:34 PDT 2015

===========PAIRED K-MER STATS===========
Total number of pairs extracted from -s W303_RAW.fof: 14985
At least one sequence/pair missing from contigs: 0
Assembled pairs: 11306 (22612 sequences)
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 2323
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 231
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 196
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 123
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 8433
	---
Total satisfied: 2446	unsatisfied: 8860

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: 11306
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 2323
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 231
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 196
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 123
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 8433
============================================
=>Scaffolding ended: Mon Apr 27 23:43:44 PDT 2015
=>Making FASTA file: Mon Apr 27 23:43:44 PDT 2015

Scaffolding executed normally Mon Apr 27 23:43:49 PDT 2015