Running: ../LINKS [v1.5]
-f S288cNANOlinks39.scaffolds.fa
-s W303_NANOCORR.fof
-d 34000
-k 15
-e 0.1
-l 5
-a 0.3
-t 6
-o 0
-b S288cNANOlinks40
-r S288cNANOlinks1.bloom
-p 0.0001

Checking W303_ONT_Nanocorr_Corrected_reads.fa...ok
Checking sequence target file S288cNANOlinks39.scaffolds.fa...ok

=>Reading contigs file, building Bloom filter: Fri May 22 19:08:04 PDT 2015
Checking Bloom filter file S288cNANOlinks1.bloom...ok
A Bloom filter was supplied (S288cNANOlinks1.bloom) and will be used instead of building a new one from -f S288cNANOlinks39.scaffolds.fa

=>Reading long reads, building hash table: Fri May 22 19:08:04 PDT 2015

Reads processed k=15, dist=34000, offset=0 nt, sliding step=6 nt:

Reads processed from file 1/1, W303_ONT_Nanocorr_Corrected_reads.fa:
105281


Extracted 109715 total 15-mer pairs

=>Reading sequence contigs (to scaffold), tracking k-mer positions: Fri May 22 19:08:10 PDT 2015

Contigs processed k=15:
7612


=>Scaffolding initiated: Fri May 22 19:08:18 PDT 2015

===========PAIRED K-MER STATS===========
Total number of pairs extracted from -s W303_NANOCORR.fof: 109715
At least one sequence/pair missing from contigs: 0
Assembled pairs: 75861 (151722 sequences)
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 48863
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 2199
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 11324
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 41
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 13434
	---
Total satisfied: 48904	unsatisfied: 26957

Breakdown by insert sizes:
--------Reads with 34000 bp inserts--------
MIN:30600 MAX:37400 as defined by 34000 * 0.1
At least one sequence/pair missing: 
Assembled pairs: 75861
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 48863
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 2199
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 11324
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 41
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 13434
============================================
=>Scaffolding ended: Fri May 22 19:08:19 PDT 2015
=>Making FASTA file: Fri May 22 19:08:19 PDT 2015

Scaffolding executed normally Fri May 22 19:08:20 PDT 2015