Running: ../LINKS [v1.5]
-f W303links26.scaffolds.fa
-s W303_RAW.fof
-d 15000
-k 15
-e 0.1
-l 5
-a 0.3
-t 6
-o 0
-b W303links27
-r W303links1.bloom
-g 0

Checking W303_rawONT_longread.fa...ok
Checking sequence target file W303links26.scaffolds.fa...ok

=>Reading contigs file, building Bloom filter: Tue Apr 28 03:03:58 PDT 2015
Checking Bloom filter file W303links1.bloom...ok
A Bloom filter was supplied (W303links1.bloom) and will be used instead of building a new one from -f W303links26.scaffolds.fa

=>Reading long reads, building hash table: Tue Apr 28 03:03:58 PDT 2015

Reads processed k=15, dist=15000, offset=0 nt, sliding step=6 nt:

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


Extracted 19257 total 15-mer pairs

=>Reading sequence contigs (to scaffold), tracking k-mer positions: Tue Apr 28 03:04:41 PDT 2015

Contigs processed k=15:
6714


=>Scaffolding initiated: Tue Apr 28 03:04:56 PDT 2015

===========PAIRED K-MER STATS===========
Total number of pairs extracted from -s W303_RAW.fof: 19257
At least one sequence/pair missing from contigs: 0
Assembled pairs: 13632 (27264 sequences)
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 3069
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 275
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 256
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 60
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 9972
	---
Total satisfied: 3129	unsatisfied: 10503

Breakdown by insert sizes:
--------Reads with 15000 bp inserts--------
MIN:13500 MAX:16500 as defined by 15000 * 0.1
At least one sequence/pair missing: 
Assembled pairs: 13632
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 3069
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 275
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 256
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 60
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 9972
============================================
=>Scaffolding ended: Tue Apr 28 03:05:07 PDT 2015
=>Making FASTA file: Tue Apr 28 03:05:07 PDT 2015

Scaffolding executed normally Tue Apr 28 03:05:13 PDT 2015