Running: /projects/rwarren_prj2/LINKS/paper/links_v1.5/LINKS [v1.5]
-f rawillATlinks3.scaffolds.fa
-s pacbio.fof
-d 20000
-k 21
-e 0.1
-l 5
-a 0.3
-t 5
-o 5
-b rawillATlinks4
-r rawillATlinks1.bloom
-p 0.0001
-x 0

Checking pacbio.fasta...ok
Checking sequence target file rawillATlinks3.scaffolds.fa...ok
Checking Bloom filter file rawillATlinks1.bloom...ok
A Bloom filter was supplied (rawillATlinks1.bloom) and will be used instead of building a new one from -f rawillATlinks3.scaffolds.fa

=>Reading long reads, building hash table: Wed Jun 17 17:27:37 PDT 2015

Reads processed k=21, dist=20000, offset=5 nt, sliding step=5 nt:

Reads processed from file 1/1, pacbio.fasta:
3448228


Extracted 26387 total 21-mer pairs

=>Reading sequence contigs (to scaffold), tracking k-mer positions: Wed Jun 17 17:31:35 PDT 2015

Contigs processed k=21:
99332


=>Scaffolding initiated: Wed Jun 17 17:34:43 PDT 2015

===========PAIRED K-MER STATS===========
Total number of pairs extracted from -s pacbio.fof: 26387
At least one sequence/pair missing from contigs: 0
Assembled pairs: 5665 (11330 sequences)
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 3614
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 288
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 276
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 236
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 1251
	---
Total satisfied: 3850	unsatisfied: 1815

Breakdown by insert sizes:
--------Reads with 20000 bp inserts--------
MIN:18000 MAX:22000 as defined by 20000 * 0.1
At least one sequence/pair missing: 
Assembled pairs: 5665
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 3614
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 288
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 276
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 236
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 1251
============================================
=>Scaffolding ended: Wed Jun 17 17:34:48 PDT 2015
=>Making FASTA file: Wed Jun 17 17:34:48 PDT 2015

Scaffolding executed normally Wed Jun 17 17:34:53 PDT 2015